Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001083962.2(TCF4):c.245G>A (p.Ser82Asn)

CA8970611

1312388 (ClinVar)

Gene: TCF4
Condition: Pitt-Hopkins syndrome
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 917e8ced-f075-4713-95ff-8b523c41717d
Approved on: 2024-08-30
Published on: 2024-12-13

HGVS expressions

NM_001083962.2:c.245G>A
NM_001083962.2(TCF4):c.245G>A (p.Ser82Asn)
NC_000018.10:g.55461078C>T
CM000680.2:g.55461078C>T
NC_000018.9:g.53128309C>T
CM000680.1:g.53128309C>T
NC_000018.8:g.51279307C>T
NG_011716.1:g.132552G>A
NG_011716.2:g.179916G>A
ENST00000354452.8:c.245G>A
ENST00000635822.2:c.245G>A
ENST00000636400.2:c.173G>A
ENST00000636751.2:c.173G>A
ENST00000637115.2:c.*135G>A
ENST00000637239.2:n.312G>A
ENST00000638154.3:c.275G>A
ENST00000674598.1:n.715G>A
ENST00000674764.1:c.119G>A
ENST00000354452.7:c.245G>A
ENST00000356073.8:c.245G>A
ENST00000398339.5:c.551G>A
ENST00000537578.5:c.173G>A
ENST00000540999.5:c.173G>A
ENST00000543082.5:c.119G>A
ENST00000562543.5:c.245G>A
ENST00000562847.5:c.8G>A
ENST00000563686.5:n.100G>A
ENST00000563824.5:c.173G>A
ENST00000563888.6:c.173G>A
ENST00000564343.5:c.173G>A
ENST00000564403.6:c.245G>A
ENST00000564999.5:c.245G>A
ENST00000565018.6:c.173G>A
ENST00000565580.3:n.174G>A
ENST00000565908.6:c.173G>A
ENST00000566279.5:c.245G>A
ENST00000566286.5:c.239G>A
ENST00000566514.5:c.206G>A
ENST00000567880.5:c.245G>A
ENST00000568147.5:c.209G>A
ENST00000568169.5:c.257G>A
ENST00000568673.5:c.173G>A
ENST00000568740.5:c.173G>A
ENST00000569357.4:c.454G>A
ENST00000616053.4:c.173G>A
ENST00000625716.2:n.175G>A
ENST00000626425.2:c.173G>A
ENST00000626595.2:c.245G>A
ENST00000627136.2:n.219G>A
ENST00000627320.2:c.*175G>A
ENST00000627685.2:c.173G>A
ENST00000627784.2:c.245G>A
ENST00000629387.2:c.245G>A
ENST00000630319.2:c.74-57560G>A
NM_001083962.1:c.245G>A
NM_001243226.2:c.551G>A
NM_001243227.1:c.173G>A
NM_001243228.1:c.245G>A
NM_001243230.1:c.239G>A
NM_001243231.1:c.119G>A
NM_001306207.1:c.173G>A
NM_003199.2:c.245G>A
NR_132985.1:n.178+8368C>T
NM_001330604.2:c.245G>A
NM_001348211.1:c.119G>A
NM_001348217.1:c.173G>A
NM_001348218.1:c.173G>A
NM_001348219.1:c.173G>A
NM_001348220.1:c.173G>A
NM_001243226.3:c.551G>A
NM_001243227.2:c.173G>A
NM_001243228.2:c.245G>A
NM_001243231.2:c.119G>A
NM_001330604.3:c.245G>A
NM_001348211.2:c.119G>A
NM_001348218.2:c.173G>A
NM_001348219.2:c.173G>A
NM_001369567.1:c.245G>A
NM_001369568.1:c.245G>A
NM_001369569.1:c.245G>A
NM_001369570.1:c.245G>A
NM_001369571.1:c.245G>A
NM_001369572.1:c.245G>A
NM_001369573.1:c.245G>A
NM_001369574.1:c.245G>A
NM_001369575.1:c.173G>A
NM_001369576.1:c.173G>A
NM_001369577.1:c.173G>A
NM_001369578.1:c.173G>A
NM_001369579.1:c.173G>A
NM_001369580.1:c.173G>A
NM_001369581.1:c.173G>A
NM_001369582.1:c.173G>A
NM_001369583.1:c.173G>A
NM_001369584.1:c.173G>A
NM_001369585.1:c.173G>A
NM_001369586.1:c.173G>A
NM_003199.3:c.245G>A
NM_001243230.2:c.239G>A
More

Likely Benign

Met criteria codes 2
BS2 BP4
Not Met criteria codes 3
BS1 BA1 PM2

Evidence Links 0

Expert Panel

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 p.Ser82Asn variant in TCF4 in gnomAD v2.1.1 is 0.00006 in African/African American population (not sufficient to meet BS1 criteria). The p.Ser82Asn variant is observed in at least 2 unaffected individuals (internal database - GeneDx and Invitae) (BS2). Computational analysis prediction tools suggest that the p.Ser82Asn variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Ser82Asn variant in TCF4 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP4). (TCF4 specifications v.3; approved on 8/30/2024)
Met criteria codes
BS2
The p.Ser82Asn variant is observed in at least 2 unaffected individuals (internal database - GeneDx and Invitae) (BS2).
BP4
Computational analysis prediction tools suggest that the p.Ser82Asn variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4).
Not Met criteria codes
BS1
The highest population minor allele frequency of the p.Ser82Asn variant in TCF4 in gnomAD v2.1.1 is 0.00006 in African/African American population (not sufficient to meet BS1 criteria).
BA1
The highest population minor allele frequency of the p.Ser82Asn variant in TCF4 in gnomAD v2.1.1 is 0.00006 in African/African American population (not sufficient to meet BA1 criteria).
PM2
The highest population minor allele frequency of the p.Ser82Asn variant in TCF4 in gnomAD v2.1.1 is 0.00006 in African/African American population (not sufficient to meet PM2 criteria).
Curation History
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