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_000260.3(MYO7A):c.1007G>A (p.Arg336His)

CA132194

43134 (ClinVar)

Gene: MYO7A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 63bd6cea-9e2a-4ad6-a8c4-5a0d13f28c7e
Approved on: 2020-11-02
Published on: 2020-11-02

HGVS expressions

NM_000260.3:c.1007G>A
NM_000260.3(MYO7A):c.1007G>A (p.Arg336His)
NM_001127179.2:c.1007G>A
NM_001127180.1:c.1007G>A
NM_000260.4:c.1007G>A
NM_001127180.2:c.1007G>A
NM_001369365.1:c.974G>A
ENST00000409619.6:c.974G>A
ENST00000409709.7:c.1007G>A
ENST00000409893.5:c.1007G>A
ENST00000458637.6:c.1007G>A
ENST00000620575.4:c.1007G>A
NC_000011.10:g.77159450G>A
CM000673.2:g.77159450G>A
NC_000011.9:g.76870496G>A
CM000673.1:g.76870496G>A
NC_000011.8:g.76548144G>A
NG_009086.1:g.36187G>A
NG_009086.2:g.36205G>A
More

Likely Benign

Met criteria codes 2
BP2 BS1_Supporting
Not Met criteria codes 1
PP3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.1007G>A (p.Arg336His) variant in MYO7A was present in 0.20% (284/127730) non-Finnish European alleles in gnomAD v2.1 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). It was identified in the homozygous state in 2 individuals, one of which was beyond the average age of onset for Usher syndrome. The variant was detected in an individual with Usher syndrome in whom a second variant was not found (PMID: 16470552). It was also identified in 2 patients with severe sensorineural hearing loss and Retinitis pigmentosa who carried other pathogenic or likely pathogenic variants thought to be causative of disease (BP2; SCV000059690.6; ClinVar IDs: 43340, 43223, 2351, 48449). The REVEL computational prediction tool produced a score of 0.734, which is above the threshold necessary to apply PP3. However, after discussion the expert panel decided not to apply PP3 based upon case level and frequency data. 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_Supporting, BP2. The c.1007G>A (Arg336His) variant was also assessed for autosomal dominant non-syndromic hearing loss. This resulted in a benign classification ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BA1, BS4, BP2.
Met criteria codes
BS1_Supporting
Present in 0.20% (284/127730) non-Finnish European alleles, 2 homozygotes in gnomAD v2.1.1 Present in 0.22% (154/60262) non-Finnish European alleles, 0 homozygotes in gnomAD v3
Not Met criteria codes
PP3
REVEL score is 0.734, which is >0.7 threshold. After expert discussion, not applied because it is conflicting with case level and frequency data.
Curation History
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