rs111033381

Positions:

chr1-215674614-C-A

Variant summary

Our verdict is Benign. Variant got -18 ACMG points: 2P and 20B. PM1BP4_StrongBP6_Very_StrongBS1BS2

The NM_206933.4(USH2A):c.13297G>T(p.Val4433Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0216 in 1,614,142 control chromosomes in the GnomAD database, including 472 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 46 hom., cov: 32)

Exomes 𝑓: 0.022 ( 426 hom. )

Consequence

USH2A
NM_206933.4 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:9O:1

Conservation

PhyloP100: -1.27

Variant links:

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]

USH2A links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -18 ACMG points.

PM1

In a domain Fibronectin type-III 29 (size 87) in uniprot entity USH2A_HUMAN there are 24 pathogenic changes around while only 2 benign (92%) in NM_206933.4

BP4

Computational evidence support a benign effect (MetaRNN=0.0023987293).

BP6

Variant 1-215674614-C-A is Benign according to our data. Variant chr1-215674614-C-A is described in ClinVar as [Benign]. Clinvar id is 48415.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-215674614-C-A is described in Lovd as [Benign]. Variant chr1-215674614-C-A is described in Lovd as [Likely_benign].

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0182 (2775/152280) while in subpopulation NFE AF= 0.0244 (1660/68022). AF 95% confidence interval is 0.0234. There are 46 homozygotes in gnomad4. There are 1397 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 46 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
USH2A	NM_206933.4 linkuse as main transcript	c.13297G>T	p.Val4433Leu	missense_variant	63/72	ENST00000307340.8	NP_996816.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
USH2A	ENST00000307340.8 linkuse as main transcript	c.13297G>T	p.Val4433Leu	missense_variant	63/72	1	NM_206933.4	ENSP00000305941	P1	O75445-1
USH2A	ENST00000674083.1 linkuse as main transcript	c.13297G>T	p.Val4433Leu	missense_variant	63/73			ENSP00000501296		O75445-3

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2775

AN:

152162

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00348

Gnomad AMI

AF:

0.143

Gnomad AMR

AF:

0.0117

Gnomad ASJ

AF:

0.0308

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00145

Gnomad FIN

AF:

0.0482

Gnomad MID

AF:

0.0285

Gnomad NFE

AF:

0.0244

Gnomad OTH

AF:

0.0134

GnomAD3 exomes

AF:

0.0191

AC:

4802

AN:

250872

Hom.:

AF XY:

0.0188

AC XY:

2543

AN XY:

135548

show subpopulations

Gnomad AFR exome

AF:

0.00332

Gnomad AMR exome

AF:

0.00605

Gnomad ASJ exome

AF:

0.0302

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.0464

Gnomad NFE exome

AF:

0.0266

Gnomad OTH exome

AF:

0.0232

GnomAD4 exome

AF:

0.0219

AC:

32020

AN:

1461862

Hom.:

426

Cov.:

AF XY:

0.0212

AC XY:

15446

AN XY:

727226

show subpopulations

Gnomad4 AFR exome

AF:

0.00290

Gnomad4 AMR exome

AF:

0.00602

Gnomad4 ASJ exome

AF:

0.0290

Gnomad4 EAS exome

AF:

0.0000252

Gnomad4 SAS exome

AF:

0.00278

Gnomad4 FIN exome

AF:

0.0481

Gnomad4 NFE exome

AF:

0.0239

Gnomad4 OTH exome

AF:

0.0229

GnomAD4 genome

AF:

0.0182

AC:

2775

AN:

152280

Hom.:

Cov.:

AF XY:

0.0188

AC XY:

1397

AN XY:

74460

show subpopulations

Gnomad4 AFR

AF:

0.00346

Gnomad4 AMR

AF:

0.0117

Gnomad4 ASJ

AF:

0.0308

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00166

Gnomad4 FIN

AF:

0.0482

Gnomad4 NFE

AF:

0.0244

Gnomad4 OTH

AF:

0.0133

Alfa

AF:

0.0231

Hom.:

Bravo

AF:

0.0157

TwinsUK

AF:

0.0245

AC:

ALSPAC

AF:

0.0231

AC:

ESP6500AA

AF:

0.00340

AC:

ESP6500EA

AF:

0.0255

AC:

219

ExAC

AF:

0.0192

AC:

2330

Asia WGS

AF:

0.00289

AC:

AN:

3478

EpiCase

AF:

0.0224

EpiControl

AF:

0.0220

ClinVar

Significance: Benign

Submissions summary: Benign:9Other:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3Other:1

Benign, criteria provided, single submitter	clinical testing	GeneDx	Mar 03, 2015	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 31, 2024	- -
not provided, no classification provided	literature only	NEI Ophthalmic Genomics Laboratory, National Institutes of Health	-	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

not specified

Benign:3

Benign, criteria provided, single submitter	clinical testing	Athena Diagnostics	Jul 10, 2020	- -
Benign, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jul 22, 2014	- -
Benign, criteria provided, single submitter	clinical testing	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	Jun 17, 2010	- -

Usher syndrome type 2A

Benign:2

Likely benign, no assertion criteria provided	clinical testing	Natera, Inc.	Nov 27, 2019	- -
Benign, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	Nov 04, 2023	- -

Retinitis pigmentosa 39

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Nov 04, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.090

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.73

CADD

Benign

1.3

DANN

Benign

0.91

DEOGEN2

Benign

0.026

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.0

FATHMM_MKL

Benign

0.064

LIST_S2

Benign

0.39

MetaRNN

Benign

0.0024

MetaSVM

Benign

-1.1

MutationAssessor

Benign

0.39

MutationTaster

Benign

1.0

N;N

PrimateAI

Benign

0.21

PROVEAN

Benign

-0.38

REVEL

Benign

0.055

Sift

Benign

0.32

Sift4G

Benign

0.33

Polyphen

0.0

Vest4

0.028

MutPred

0.39

Loss of catalytic residue at V4433 (P = 0.1009);

MPC

0.030

ClinPred

0.016

GERP RS

-0.13

Varity_R

0.040

gMVP

0.22

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over