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_206933.2(USH2A):c.15297+3A>G

CA143392

48459 (ClinVar)

Gene: USH2A
Condition: Usher syndrome
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 801f4ee3-5d91-4c86-ba72-2ecc81250c22
Approved on: 2018-09-14
Published on: 2019-07-17

HGVS expressions

NM_206933.2:c.15297+3A>G
NM_206933.2(USH2A):c.15297+3A>G
NC_000001.11:g.215634456T>C
CM000663.2:g.215634456T>C
NC_000001.10:g.215807798T>C
CM000663.1:g.215807798T>C
NC_000001.9:g.213874421T>C
NG_009497.1:g.793941A>G
NM_206933.3:c.15297+3A>G
ENST00000307340.7:c.15297+3A>G

Benign

Met criteria codes 1
BA1
Not Met criteria codes 22
BS2 BS1 BS4 BP7 BP5 BP4 BP3 BP2 PS1 PS4 PS2 PS3 PP3 PP1 PP4 PM2 PM6 PM5 PM4 PM1 PM3 PVS1

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.15297+3A>G variant in the USH2A gene is 0.99% (265/24032) of African chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1).
Met criteria codes
BA1
ExAC filtering allele frequency 0.009091 (African) SA 9/14/18: gnomAD MAF 1.1% including 2 hom individuals
Not Met criteria codes
BS2
This variant was found in 2 homozygotes in gnomAD. if the variant caused LOF of the protein, it would have caused Usher syndrome which has childhood onset.
BS1
ExAC filtering allele frequency 0.009091 (African) SA 9/14/18: gnomAD MAF 1.1% including 2 hom individuals
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
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
BP4
MaxEntScan does not have clear prediction on splicing. It seems to decrease the chance of splicing, but not completely.
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
PS1
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
PP3
MaxEntScan does not have clear prediction on splicing. It seems to decrease the chance of splicing, but not completely.
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
PM2
ExAC filtering allele frequency 0.009091 (African) SA 9/14/18: gnomAD MAF 1.1% including 2 hom individuals
PM6
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
PVS1
This variant is not predicted and has not been shown to impact splicing. If it did, it would cause a frameshift by deleting exon 70/72.
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