rs59174500

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 2P and 16B. PM1BP4_StrongBP6_Very_StrongBS2

The ENST00000307340.8(USH2A):​c.8458G>A​(p.Val2820Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000688 in 1,614,010 control chromosomes in the GnomAD database, including 7 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 Likely benign (★★).

Frequency

Genomes: 𝑓 0.0037 ( 2 hom., cov: 32)
Exomes 𝑓: 0.00038 ( 5 hom. )

Consequence

USH2A
ENST00000307340.8 missense

Scores

18

Clinical Significance

Benign/Likely benign criteria provided, multiple submitters, no conflicts B:8

Conservation

PhyloP100: 0.183
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

PM1
In a domain Fibronectin type-III 15 (size 103) in uniprot entity USH2A_HUMAN there are 16 pathogenic changes around while only 6 benign (73%) in ENST00000307340.8
BP4
Computational evidence support a benign effect (MetaRNN=0.010608584).
BP6
Variant 1-215878864-C-T is Benign according to our data. Variant chr1-215878864-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 178648.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-215878864-C-T is described in Lovd as [Benign].
BS2
High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
USH2ANM_206933.4 linkuse as main transcriptc.8458G>A p.Val2820Ile missense_variant 42/72 ENST00000307340.8 NP_996816.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
USH2AENST00000307340.8 linkuse as main transcriptc.8458G>A p.Val2820Ile missense_variant 42/721 NM_206933.4 ENSP00000305941 P1O75445-1
USH2AENST00000674083.1 linkuse as main transcriptc.8458G>A p.Val2820Ile missense_variant 42/73 ENSP00000501296 O75445-3

Frequencies

GnomAD3 genomes
AF:
0.00364
AC:
554
AN:
152076
Hom.:
2
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0124
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00210
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00316
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00287
GnomAD3 exomes
AF:
0.00104
AC:
262
AN:
251214
Hom.:
3
AF XY:
0.000722
AC XY:
98
AN XY:
135784
show subpopulations
Gnomad AFR exome
AF:
0.0130
Gnomad AMR exome
AF:
0.00116
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.000109
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000528
Gnomad OTH exome
AF:
0.000490
GnomAD4 exome
AF:
0.000380
AC:
555
AN:
1461816
Hom.:
5
Cov.:
32
AF XY:
0.000327
AC XY:
238
AN XY:
727206
show subpopulations
Gnomad4 AFR exome
AF:
0.0110
Gnomad4 AMR exome
AF:
0.00112
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.0000504
Gnomad4 SAS exome
AF:
0.0000348
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000728
Gnomad4 OTH exome
AF:
0.000844
GnomAD4 genome
AF:
0.00365
AC:
556
AN:
152194
Hom.:
2
Cov.:
32
AF XY:
0.00348
AC XY:
259
AN XY:
74416
show subpopulations
Gnomad4 AFR
AF:
0.0124
Gnomad4 AMR
AF:
0.00209
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00284
Alfa
AF:
0.00150
Hom.:
1
Bravo
AF:
0.00447
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.0123
AC:
54
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00120
AC:
146
Asia WGS
AF:
0.000577
AC:
3
AN:
3478
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Benign/Likely benign
Submissions summary: Benign:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingGeneDxMay 03, 2019- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpFeb 01, 2024- -
Usher syndrome type 2A Benign:2
Likely benign, criteria provided, single submitterclinical testingGenome-Nilou LabNov 04, 2023- -
Benign, no assertion criteria providedclinical testingNatera, Inc.Dec 08, 2019- -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineMay 07, 2012Val2820Ile in Exon 42 of USH2A: This variant is not expected to have clinical si gnificance because it has been identified in 1.4% (54/3738) of African American chromosomes from a broad population by the NHLBI Exome Sequencing Project (http: //evs.gs.washington.edu/EVS; dbSNP rs59174500). -
Usher syndrome type 2A;C3151138:Retinitis pigmentosa 39 Benign:1
Likely benign, criteria provided, single submitterclinical testingFulgent Genetics, Fulgent GeneticsMay 20, 2022- -
Retinitis pigmentosa 39 Benign:1
Likely benign, criteria provided, single submitterclinical testingGenome-Nilou LabNov 04, 2023- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.069
BayesDel_addAF
Benign
-0.68
T
BayesDel_noAF
Benign
-0.73
CADD
Benign
6.3
DANN
Benign
0.37
DEOGEN2
Benign
0.042
T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.2
FATHMM_MKL
Benign
0.063
N
LIST_S2
Benign
0.46
T
MetaRNN
Benign
0.011
T
MetaSVM
Benign
-1.1
T
MutationAssessor
Benign
-1.1
N
MutationTaster
Benign
1.0
N;N
PrimateAI
Benign
0.24
T
PROVEAN
Benign
0.10
N
REVEL
Benign
0.019
Sift
Benign
0.54
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.067
MVP
0.41
MPC
0.027
ClinPred
0.0012
T
GERP RS
0.065
Varity_R
0.024
gMVP
0.17

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.

Other links and lift over

dbSNP: rs59174500; hg19: chr1-216052206; API