rs1410059

Variant summary

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

The NM_001034954.3(SORBS1):​c.810+1656A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.521 in 151,874 control chromosomes in the GnomAD database, including 20,891 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 0.52 ( 20891 hom., cov: 31)

Consequence

SORBS1
NM_001034954.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.483
Variant links:
Genes affected
SORBS1 (HGNC:14565): (sorbin and SH3 domain containing 1) This gene encodes a CBL-associated protein which functions in the signaling and stimulation of insulin. Mutations in this gene may be associated with human disorders of insulin resistance. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
SORBS1NM_001034954.3 linkuse as main transcriptc.810+1656A>G intron_variant ENST00000371247.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
SORBS1ENST00000371247.7 linkuse as main transcriptc.810+1656A>G intron_variant 5 NM_001034954.3 P3Q9BX66-1

Frequencies

GnomAD3 genomes
AF:
0.521
AC:
79074
AN:
151756
Hom.:
20865
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.585
Gnomad AMI
AF:
0.496
Gnomad AMR
AF:
0.499
Gnomad ASJ
AF:
0.549
Gnomad EAS
AF:
0.597
Gnomad SAS
AF:
0.678
Gnomad FIN
AF:
0.445
Gnomad MID
AF:
0.652
Gnomad NFE
AF:
0.480
Gnomad OTH
AF:
0.541
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.521
AC:
79143
AN:
151874
Hom.:
20891
Cov.:
31
AF XY:
0.522
AC XY:
38757
AN XY:
74212
show subpopulations
Gnomad4 AFR
AF:
0.585
Gnomad4 AMR
AF:
0.499
Gnomad4 ASJ
AF:
0.549
Gnomad4 EAS
AF:
0.596
Gnomad4 SAS
AF:
0.679
Gnomad4 FIN
AF:
0.445
Gnomad4 NFE
AF:
0.480
Gnomad4 OTH
AF:
0.543
Alfa
AF:
0.492
Hom.:
5338
Bravo
AF:
0.520
Asia WGS
AF:
0.629
AC:
2184
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
2.8
DANN
Benign
0.72

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: rs1410059; hg19: chr10-97172595; API