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

  • See Evidence submitted by expert panel for details.

Variant: NM_194248.3(OTOF):c.4463A>T (p.Asp1488Val)

CA142888

48235 (ClinVar)

Gene: OTOF
Condition: nonsyndromic genetic deafness
Inheritance Mode: Autosomal recessive inheritance
UUID: a8aca6bb-9e6a-4371-abb7-4d5ac7d567c7
Approved on: 2021-04-20
Published on: 2022-05-13

HGVS expressions

NM_194248.3:c.4463A>T
NM_194248.3(OTOF):c.4463A>T (p.Asp1488Val)
NC_000002.12:g.26466751T>A
CM000664.2:g.26466751T>A
NC_000002.11:g.26689619T>A
CM000664.1:g.26689619T>A
NC_000002.10:g.26543123T>A
NG_009937.1:g.96948A>T
ENST00000272371.7:c.4463A>T
ENST00000339598.8:c.2162A>T
ENST00000402415.8:c.2222A>T
ENST00000272371.6:c.4463A>T
ENST00000338581.10:c.2162A>T
ENST00000339598.7:c.2162A>T
ENST00000402415.7:c.2393A>T
ENST00000403946.7:c.4463A>T
NM_001287489.1:c.4463A>T
NM_004802.3:c.2162A>T
NM_194248.2:c.4463A>T
NM_194322.2:c.2393A>T
NM_194323.2:c.2162A>T
NM_001287489.2:c.4463A>T
NM_004802.4:c.2162A>T
NM_194322.3:c.2393A>T
NM_194323.3:c.2162A>T
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Uncertain Significance

Met criteria codes 2
PP3 BS1_Supporting

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 (the lower threshold of the 95% of 49/35,440) of the c.4463A>T (p.Asp1488Val) variant in OTOF is 0.107% for Latino/Admixed American alleles in gnomAD v2, which is a higher frequency than would be expected for an autosomal recessive pathogenic variant based on the thresholds defined by the ClinGen Hearing Loss Expert Panel (BS1_Supporting). The REVEL computational prediction tool produced a score of 0.805, which is above the threshold necessary to apply PP3. While this variant has been observed in at least 6 probands with hearing loss, none of these individuals had a second variant identified in OTOF (Partners Laboratory for Molecular Medicine internal data, ClinVar SCV000065239.6). In summary, the clinical significance of this variant is uncertain. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, PP3.
Met criteria codes
PP3
REVEL 0.805. MaxEntScan does not predict an impact to splicing. Four mammals have Glu at this site; none have Val.
BS1_Supporting
Present in 0.138% (49/35,440) of Latino/Admixed American alleles in gnomAD v2 (lower bound of 95% CI is 0.107%).
Curation History
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