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]
Link to SEPIO compliant JSON-LD document
  • See Evidence submitted by expert panel for details.

Variant: NM_004700.3(KCNQ4):c.720C>G (p.Thr240=)

CA10576423

227469 (ClinVar)

Gene: KCNQ4
Condition: hearing loss
Inheritance Mode: Autosomal dominant inheritance
Link to MONDO
UUID: 8cd85444-a428-437c-a5b7-582156401d13

HGVS expressions

NM_004700.3:c.720C>G
NM_004700.3(KCNQ4):c.720C>G (p.Thr240=)
NC_000001.11:g.40819358C>G
CM000663.2:g.40819358C>G
NC_000001.10:g.41285030C>G
CM000663.1:g.41285030C>G
NC_000001.9:g.41057617C>G
NG_008139.1:g.40347C>G
NG_008139.2:g.40347C>G
NM_172163.2:c.720C>G
NM_004700.4:c.720C>G
ENST00000347132.9:c.720C>G
ENST00000443478.3:n.406C>G
ENST00000506017.1:n.39C>G
ENST00000509682.6:n.720C>G

Likely Benign

Met criteria codes 2
BP7 BP4
Not Met criteria codes 20
PS1 PS3 PS4 PS2 BP5 BP3 BP2 PP3 PP1 PP4 BA1 PM6 PVS1 PM5 PM4 PM1 PM3 BS2 BS1 BS4

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The silent p.Thr240= variant in KCNQ4 is not predicted by computational tools to impact splicing (BP7. BP4). The variant is absent from the Genome Aggregation Database (http://gnomad.broadinstitute.org), however this is not considered evidence against a likely benign classification. In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied: BP7, BP4.
Met criteria codes
BP7
Silent with no predicted impact. Variant is 4 codons from splice site. Not predicted to impact splicing by any predictors in Alamut, notably MaxEntScan
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Not Met criteria codes
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Absent from gnomAD with 100x median coverage
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
Absent from gnomAD with 100x median coverage
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2018-09-28
Published on: 2019-07-17
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