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]
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  • See Evidence submitted by expert panel for details.

Variant: NM_005422.2(TECTA):c.3492C>T (p.Thr1164=)

CA182519

178539 (ClinVar)

Gene: TECTA
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 204ea045-9b19-4698-b5bd-11e5ab2a89f9
Approved on: 2019-02-13
Published on: 2019-07-17

HGVS expressions

NM_005422.2:c.3492C>T
NM_005422.2(TECTA):c.3492C>T (p.Thr1164=)
NM_005422.2:n.3492C>T
ENST00000264037.2:n.3492C>T
ENST00000392793.5:c.3492C>T
NC_000011.10:g.121137971C>T
CM000673.2:g.121137971C>T
NC_000011.9:g.121008680C>T
CM000673.1:g.121008680C>T
NC_000011.8:g.120513890C>T
NG_011633.1:g.40306C>T

Likely Benign

Met criteria codes 3
BS1 BP4 BP7
Not Met criteria codes 20
BS2 PVS1 BS4 BP2 BP3 BP5 PS4 PS2 PS3 PS1 BA1 PP3 PP1 PP4 PM3 PM1 PM4 PM5 PM2 PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The filtering allele frequency of the c.3492C>T (p.Thr1164=) variant in the TECTA gene is 0.423% for African chromosomes by gnomAD (123/23960) with 95% CI), which is a high enough frequency to be classified as likely benign based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BS1). The silent p.Thr1164= variant in TECTA is not predicted by MaxEntScan to impact splicing (BP7, BP4). In summary, this variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1, BP7, BP4.
Met criteria codes
BS1
Variant identified in 0.472 % of Arican alleles (113/23960) in gnomAD. This meets the criteria for AR BS1 as TECTA has been associated with AD and AR variants. AR BA1 cutoff is 0.5%
BP4
Variant is not predicted to impact splicing or AA sequence
BP7
Variant meets BP7
Not Met criteria codes
BS2
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
BS4
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
BP3
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
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
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
Variant identified in 0.472 % of Arican alleles (113/23960) in gnomAD. This meets the criteria for AR BS1 as TECTA has been associated with AD and AR variants. AR BA1 cutoff is 0.5%
PP3
Variant is not predicted to impact splicing or AA sequence
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
PM3
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
PM4
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
PM2
Variant identified in 0.472 % of Arican alleles (113/23960) in gnomAD. This meets the criteria for AR BS1 as TECTA has been associated with AD and AR variants. AR BA1 cutoff is 0.5%
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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