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rs7532570

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The NM_206933.4(USH2A):c.785-3273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0529 in 152,134 control chromosomes in the GnomAD database, including 294 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 0.053 ( 294 hom., cov: 32)

Consequence

USH2A
NM_206933.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.331
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 -10 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.26).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0756 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
USH2ANM_206933.4 linkuse as main transcriptc.785-3273T>C intron_variant ENST00000307340.8
USH2ANM_007123.6 linkuse as main transcriptc.785-3273T>C intron_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
USH2AENST00000307340.8 linkuse as main transcriptc.785-3273T>C intron_variant 1 NM_206933.4 P1O75445-1
USH2AENST00000366942.3 linkuse as main transcriptc.785-3273T>C intron_variant 1 O75445-2
USH2AENST00000674083.1 linkuse as main transcriptc.785-3273T>C intron_variant O75445-3

Frequencies

GnomAD3 genomes
AF:
0.0529
AC:
8041
AN:
152016
Hom.:
293
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0155
Gnomad AMI
AF:
0.0559
Gnomad AMR
AF:
0.0479
Gnomad ASJ
AF:
0.0979
Gnomad EAS
AF:
0.00386
Gnomad SAS
AF:
0.0707
Gnomad FIN
AF:
0.0470
Gnomad MID
AF:
0.108
Gnomad NFE
AF:
0.0774
Gnomad OTH
AF:
0.0613
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0529
AC:
8047
AN:
152134
Hom.:
294
Cov.:
32
AF XY:
0.0518
AC XY:
3853
AN XY:
74386
show subpopulations
Gnomad4 AFR
AF:
0.0154
Gnomad4 AMR
AF:
0.0478
Gnomad4 ASJ
AF:
0.0979
Gnomad4 EAS
AF:
0.00387
Gnomad4 SAS
AF:
0.0712
Gnomad4 FIN
AF:
0.0470
Gnomad4 NFE
AF:
0.0774
Gnomad4 OTH
AF:
0.0635
Alfa
AF:
0.0628
Hom.:
180
Bravo
AF:
0.0505
Asia WGS
AF:
0.0620
AC:
216
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.26
Cadd
Benign
15
Dann
Benign
0.84

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: rs7532570; hg19: chr1-216504269; API