Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

Variant: NM_001083962.2(TCF4):c.790-9T>C

Curation Version - 1.0
Curation History
JSON LD for Version 1.0

CA8970387

282017 (ClinVar)

Gene: TCF4

Condition: Pitt-Hopkins syndrome

Inheritance Mode: Autosomal dominant inheritance

Link to MONDO

UUID: 7ff2ead1-7309-4770-986a-cbc6317d1851

Approved on: 2024-08-30

Published on: 2024-11-15

HGVS expressions

NM_001083962.2:c.790-9T>C

NM_001083962.2(TCF4):c.790-9T>C

NC_000018.10:g.55269972A>G

CM000680.2:g.55269972A>G

NC_000018.9:g.52937203A>G

CM000680.1:g.52937203A>G

NC_000018.8:g.51088201A>G

NG_011716.1:g.323658T>C

NG_011716.2:g.371022T>C

ENST00000354452.8:c.790-9T>C

ENST00000630720.3:c.310-9T>C

ENST00000635822.2:c.790-9T>C

ENST00000635990.2:n.470-9T>C

ENST00000636400.2:c.718-9T>C

ENST00000636751.2:c.*498-9T>C

ENST00000636822.2:c.400-9T>C

ENST00000637115.2:c.*680-9T>C

ENST00000637169.2:c.142-9T>C

ENST00000637239.2:n.857-9T>C

ENST00000637250.2:n.484-9T>C

ENST00000637923.2:c.388-9T>C

ENST00000638154.3:c.820-9T>C

ENST00000643689.1:c.400-9T>C

ENST00000674764.1:c.*401-9T>C

ENST00000675707.1:c.400-9T>C

ENST00000354452.7:c.790-9T>C

ENST00000356073.8:c.790-9T>C

ENST00000398339.5:c.1096-9T>C

ENST00000457482.7:c.310-9T>C

ENST00000537578.5:c.718-9T>C

ENST00000537856.7:c.400-9T>C

ENST00000540999.5:c.718-9T>C

ENST00000543082.5:c.664-9T>C

ENST00000544241.6:c.577-9T>C

ENST00000561831.7:c.310-9T>C

ENST00000561992.5:c.400-9T>C

ENST00000562030.3:c.400-9T>C

ENST00000562607.5:c.400-9T>C

ENST00000562680.5:n.881-9T>C

ENST00000563686.5:n.645-9T>C

ENST00000563760.5:n.382-9T>C

ENST00000564228.5:c.577-9T>C

ENST00000564403.6:c.808-9T>C

ENST00000564999.5:c.790-9T>C

ENST00000565018.6:c.538-9T>C

ENST00000566279.5:c.610-9T>C

ENST00000566286.5:c.784-9T>C

ENST00000566514.5:c.751-9T>C

ENST00000566777.5:c.400-9T>C

ENST00000567880.5:c.610-9T>C

ENST00000568169.5:c.802-9T>C

ENST00000568673.5:c.718-9T>C

ENST00000568740.5:c.715-9T>C

ENST00000569012.5:c.400-9T>C

ENST00000570146.3:c.54-9T>C

ENST00000570177.6:c.400-9T>C

ENST00000570287.6:c.310-9T>C

ENST00000616053.4:c.538-9T>C

ENST00000625849.2:n.650-9T>C

ENST00000625925.2:c.400-9T>C

ENST00000626584.2:c.142-9T>C

ENST00000627136.2:n.524-8439T>C

ENST00000628078.2:c.400-9T>C

ENST00000628636.2:c.400-9T>C

ENST00000628689.2:c.176-9T>C

ENST00000629343.2:c.400-9T>C

ENST00000629387.2:c.790-9T>C

ENST00000630268.2:c.400-9T>C

ENST00000630319.2:c.559-9T>C

ENST00000630720.2:c.310-9T>C

ENST00000630828.2:c.580-9T>C

NM_001083962.1:c.790-9T>C

NM_001243226.2:c.1096-9T>C

NM_001243227.1:c.718-9T>C

NM_001243228.1:c.808-9T>C

NM_001243230.1:c.784-9T>C

NM_001243231.1:c.664-9T>C

NM_001243232.1:c.577-9T>C

NM_001243233.1:c.400-9T>C

NM_001243234.1:c.310-9T>C

NM_001243235.1:c.310-9T>C

NM_001243236.1:c.310-9T>C

NM_001306207.1:c.718-9T>C

NM_001306208.1:c.577-9T>C

NM_003199.2:c.790-9T>C

NM_001330604.2:c.790-9T>C

NM_001330605.2:c.400-9T>C

NM_001348211.1:c.664-9T>C

NM_001348212.1:c.400-9T>C

NM_001348213.1:c.400-9T>C

NM_001348214.1:c.310-9T>C

NM_001348215.1:c.142-9T>C

NM_001348216.1:c.310-9T>C

NM_001348217.1:c.718-9T>C

NM_001348218.1:c.718-9T>C

NM_001348219.1:c.718-9T>C

NM_001348220.1:c.715-9T>C

NM_001243226.3:c.1096-9T>C

NM_001243227.2:c.718-9T>C

NM_001243228.2:c.808-9T>C

NM_001243231.2:c.664-9T>C

NM_001243233.2:c.400-9T>C

NM_001243234.2:c.310-9T>C

NM_001243235.2:c.310-9T>C

NM_001243236.2:c.310-9T>C

NM_001330604.3:c.790-9T>C

NM_001330605.3:c.400-9T>C

NM_001348211.2:c.664-9T>C

NM_001348212.2:c.400-9T>C

NM_001348213.2:c.400-9T>C

NM_001348214.2:c.310-9T>C

NM_001348215.2:c.142-9T>C

NM_001348216.2:c.310-9T>C

NM_001348218.2:c.718-9T>C

NM_001348219.2:c.718-9T>C

NM_001369567.1:c.790-9T>C

NM_001369568.1:c.790-9T>C

NM_001369569.1:c.787-9T>C

NM_001369570.1:c.787-9T>C

NM_001369571.1:c.790-9T>C

NM_001369572.1:c.790-9T>C

NM_001369573.1:c.787-9T>C

NM_001369574.1:c.790-9T>C

NM_001369575.1:c.718-9T>C

NM_001369576.1:c.715-9T>C

NM_001369577.1:c.718-9T>C

NM_001369578.1:c.715-9T>C

NM_001369579.1:c.718-9T>C

NM_001369580.1:c.718-9T>C

NM_001369581.1:c.715-9T>C

NM_001369582.1:c.718-9T>C

NM_001369583.1:c.718-9T>C

NM_001369584.1:c.715-9T>C

NM_001369585.1:c.715-9T>C

NM_001369586.1:c.718-9T>C

NM_003199.3:c.790-9T>C

NM_001243230.2:c.784-9T>C

Benign

BP5_Strong BA1 BS2

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TCF4 Version 3.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The highest population minor allele frequency of the c.790-9T>C variant in TCF4 in gnomAD v4.1 is 0.006579 in the Amish population, which is higher than the ClinGen Rett and Angelman-like Disorders VCEP threshold (≥0.0003) for BA1, and therefore meets this criterion (BA1). The c.790-9T>C variant is observed in at least 2 unaffected individuals (internal database - GeneDx) (BS2). The c.790-9T>C variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx) (BP5_Strong). In summary, the c.790-9T>C variant in TCF4 is classified as benign based on the ACMG/AMP criteria (BA1, BS2, BP5_Strong).

BP5_Strong

The c.790-9T>C variant is found in at least 3 patients with an alternate molecular basis of disease (internal database - GeneDx) (BP5_Strong).

BA1

BS2

The c.790-9T>C variant is observed in at least 2 unaffected individuals (internal database - GeneDx) (BS2).

Curation History

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