rs146824138

chr1-216289285-C-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 4P and 12B. PM1 PM2 BP4_Strong BP6_Very_Strong

The NM_206933.4(USH2A):c.1966G>A(p.Asp656Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000772 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★★).

• Frequency:
  • Genomes: 𝑓 0.00068 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00078 (0 hom.)
• Consequence: USH2A NM_206933.4 missense
• Clinical Significance: Likely benign reviewed by expert panel U:10 B:6
• Conservation: PhyloP100: 2.50

Genes affected

USH2A (HGNC:12601): (usherin) This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• PM1: In a hotspot region, there are 4 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 1 benign, 6 uncertain in NM_206933.4
• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.051619977).
• BP6: Variant 1-216289285-C-T is Benign according to our data. Variant chr1-216289285-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 48481.Status of the report is reviewed_by_expert_panel, 3 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
USH2A	NM_206933.4	c.1966G>A	p.Asp656Asn	missense_variant	11/72	ENST00000307340.8
USH2A	NM_007123.6	c.1966G>A	p.Asp656Asn	missense_variant	11/21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
USH2A	ENST00000307340.8	c.1966G>A	p.Asp656Asn	missense_variant	11/72	1	NM_206933.4	P1
USH2A	ENST00000366942.3	c.1966G>A	p.Asp656Asn	missense_variant	11/21	1
USH2A	ENST00000674083.1	c.1966G>A	p.Asp656Asn	missense_variant	11/73

Frequencies

GnomAD3 genomes AF: 0.000677 AC: 103 AN: 152146 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000196

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00160

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000605 AC: 152 AN: 251290 Hom.: 0 AF XY: 0.000545 AC XY: 74 AN XY: 135806

Gnomad AFR exome AF: 0.000308

Gnomad AMR exome AF: 0.000173

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000554

Gnomad NFE exome AF: 0.00111

Gnomad OTH exome AF: 0.000489

GnomAD4 exome AF: 0.000782 AC: 1143 AN: 1461572 Hom.: 0 Cov.: 31 AF XY: 0.000740 AC XY: 538 AN XY: 727092

Gnomad4 AFR exome AF: 0.000179

Gnomad4 AMR exome AF: 0.000179

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000543

Gnomad4 NFE exome AF: 0.000964

Gnomad4 OTH exome AF: 0.000464

GnomAD4 genome AF: 0.000676 AC: 103 AN: 152264 Hom.: 0 Cov.: 32 AF XY: 0.000672 AC XY: 50 AN XY: 74460

Gnomad4 AFR AF: 0.000192

Gnomad4 AMR AF: 0.000196

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00160

Gnomad4 NFE AF: 0.00110

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000869 Hom.: 0

Bravo AF: 0.000574

TwinsUK AF: 0.00108 AC: 4

ALSPAC AF: 0.000519 AC: 2

ESP6500AA AF: 0.000227 AC: 1

ESP6500EA AF: 0.00174 AC: 15

ExAC AF: 0.000758 AC: 92

EpiCase AF: 0.000872

EpiControl AF: 0.000889

ClinVar

Significance: Likely benign

Submissions summary: Uncertain:10 Benign:6

Revision: reviewed by expert panel

Submissions by phenotype

not provided Uncertain:3 Benign:2

Likely benign, criteria provided, single submitter	clinical testing	Invitae	Jan 24, 2024	- -
Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 04, 2020	In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 16963483, 29767709, 28041643, 30245029, 32707200) -
Uncertain significance, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -
Uncertain significance, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Uncertain significance, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2021	- -

Usher syndrome type 2A Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Oct 27, 2021	NM_206933.2(USH2A):c.1966G>A(D656N) is a missense variant classified as a variant of uncertain significance in the context of USH2A-related disorders. D656N has been observed in cases with relevant disease (PMID: 16963483, 28041643, 31429209). Functional assessments of this variant are not available in the literature. D656N has been observed in population frequency databases (gnomAD: NFE 0.11%). In summary, there is insufficient evidence to classify NM_206933.2(USH2A):c.1966G>A(D656N) as pathogenic or benign. Please note: this variant was assessed in the context of healthy population screening. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Retinitis pigmentosa Uncertain:2

Uncertain significance, no assertion criteria provided	research	NIHR Bioresource Rare Diseases, University of Cambridge	Jan 01, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Amblyopia;C0431399:Familial aplasia of the vermis;C0454644:Delayed speech and language development;C1842688:Hypoplasia of the brainstem;C1854301:Motor delay;C1865866:Congenital sensorineural hearing impairment;C4022154:Cerebellar hemisphere hypoplasia;C5231391:Congenital cerebellar hypoplasia Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Centre for Mendelian Genomics, University Medical Centre Ljubljana

Jan 01, 2017

- -

Retinal dystrophy Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Blueprint Genetics

Nov 13, 2018

- -

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Jun 10, 2022

The p.Asp656Asn variant in USH2A has been reported in 3 individuals with Usher syndrome and 1 individual with hearing loss (Cremers 2007 PMID: 16963483, LMM data). However, the role of this variant in these 3 individuals remains inconclusive for various reasons (2 of the individuals with Usher syndrome [LMM data] had two pathogenic variants in a different gene that explained disease, the study that reported 1 individual with Usher syndrome did not comment on whether or not a second variant was present [Cremers 2007 PMID: 16963483], and the individual with hearing loss [LMM data], did not harbor a pathogenic variant on the remaining copy of USH2A). In addition, the p.Asp656Asn variant has been reported in 1 individual with inherited isolated retinitis pigmentosa along with 2 additional USH2A variants (p.Thr3667Pro and p.Gln3326X; Carss 2017 PMID: 28041643); however, phase was undetermined. This variant was also found in one individual with retinal disease and 1 individual with uveitis (Holtan 2020 PMID: 31429209, Li 2021 PMID: 32707200). This variant has also been identified in 0.1% (145/129044) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org) and is reported in ClinVar (Variation ID: 48481) as likely benign by the ClinGen Hearing Loss Expert Panel. Additionally, computational prediction analysis using the metapredictor tool REVEL suggests that the variant may not impact the protein. In summary, the high MAF, presence in multiple cases with an alternate cause, and the computational data suggest that it is more likely to be benign. ACMG/AMP Criteria applied: BS1_Supporting, BP4. -

Usher syndrome Benign:1

Likely benign, reviewed by expert panel

curation

ClinGen Hearing Loss Variant Curation Expert Panel

May 25, 2020

The allele frequency of the c.1966G>A (p.Asp656Asn) variant in USH2A is 0.095% (16/10466 CI 95%) of Finnish alleles in gnomAD v3., 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 variant has been identified in 3 probands with hearing loss and 2 probands with Usher syndrome (SCV000065500.6; PMID: 16963483); however an alternate cause of hearing loss in other genes was identified in 3 probands (SCV000065500.6), and a second variant in USH2A was not identified in the other two probands (SCV000065500.6; PMID: 16963483). Finally, in the last proband, another likely benign variant was identified with phasing unknown (SCV000065500.6). Altogether, this evidence does not meet the criteria set to apply PM3_Supporting. Additionally, computational prediction analysis using the metapredictor tool REVEL suggests that the variant may not impact the protein (BP4). In summary, the c.1966G>A (p.Asp656Asn) variant meets criteria to be classified as likely benign. ACMG/AMP criteria applied, as specified by the Hearing Loss Expert Panel: BS1_Supporting, BP4. -

Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Jul 28, 2021

- -

USH2A-related condition Benign:1

Likely benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Apr 20, 2021

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Benign	-0.52	T
BayesDel_noAF	Benign	-0.56
Cadd	Benign	16
Dann	Uncertain	0.99
DEOGEN2	Benign	0.076	T;.
Eigen	Benign	-0.27
Eigen_PC	Benign	-0.15
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.62	T;T
M_CAP	Benign	0.025	D
MetaRNN	Benign	0.052	T;T
MetaSVM	Benign	-0.97	T
MutationAssessor	Benign	1.8	L;L
MutationTaster	Benign	0.98	D;D;D
PrimateAI	Benign	0.40	T
PROVEAN	Benign	-2.0	N;N
REVEL	Benign	0.073
Sift	Benign	0.040	D;T
Sift4G	Uncertain	0.030	D;T
Polyphen		0.14	B;B
Vest4		0.74
MVP		0.90
MPC		0.049
ClinPred		0.035	T
GERP RS		4.2
Varity_R		0.063
gMVP		0.53

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs146824138; hg19: chr1-216462627;