rs10495006

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_206933.4(USH2A):​c.9372-1871T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0359 in 151,990 control chromosomes in the GnomAD database, including 169 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.036 ( 169 hom., cov: 32)

Consequence

USH2A
NM_206933.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.701
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
USH2ANM_206933.4 linkuse as main transcriptc.9372-1871T>C intron_variant ENST00000307340.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
USH2AENST00000307340.8 linkuse as main transcriptc.9372-1871T>C intron_variant 1 NM_206933.4 P1O75445-1
USH2AENST00000674083.1 linkuse as main transcriptc.9372-1871T>C intron_variant O75445-3

Frequencies

GnomAD3 genomes
AF:
0.0360
AC:
5467
AN:
151872
Hom.:
168
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0102
Gnomad AMI
AF:
0.0197
Gnomad AMR
AF:
0.0537
Gnomad ASJ
AF:
0.00865
Gnomad EAS
AF:
0.152
Gnomad SAS
AF:
0.0768
Gnomad FIN
AF:
0.00660
Gnomad MID
AF:
0.0443
Gnomad NFE
AF:
0.0419
Gnomad OTH
AF:
0.0445
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0359
AC:
5464
AN:
151990
Hom.:
169
Cov.:
32
AF XY:
0.0364
AC XY:
2703
AN XY:
74284
show subpopulations
Gnomad4 AFR
AF:
0.0102
Gnomad4 AMR
AF:
0.0535
Gnomad4 ASJ
AF:
0.00865
Gnomad4 EAS
AF:
0.152
Gnomad4 SAS
AF:
0.0766
Gnomad4 FIN
AF:
0.00660
Gnomad4 NFE
AF:
0.0420
Gnomad4 OTH
AF:
0.0469
Alfa
AF:
0.0324
Hom.:
18
Bravo
AF:
0.0369
Asia WGS
AF:
0.119
AC:
412
AN:
3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.8
DANN
Benign
0.65

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: rs10495006; hg19: chr1-215992408; API