rs732102

Variant names:

• chr10-95432788-G-A
• rs732102
• NM_001034954.3:c.173-212C>T

Your query was ambiguous. Multiple possible variants found:

• chr10-95432788-G-A
• chr10-95432788-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001034954.3(SORBS1):​c.173-212C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,816 control chromosomes in the GnomAD database, including 12,123 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 0.39 (12123 hom., cov: 30)
• Consequence: SORBS1 NM_001034954.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 3 publications found

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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.635 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SORBS1	NM_001034954.3	c.173-212C>T		intron_variant	Intron 5 of 32	ENST00000371247.7	NP_001030126.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SORBS1	ENST00000371247.7	c.173-212C>T		intron_variant	Intron 5 of 32	5	NM_001034954.3	ENSP00000360293.2

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59460 AN: 151698 Hom.: 12102 Cov.: 30

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.376

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.654

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.311

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.366

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.392 AC: 59542 AN: 151816 Hom.: 12123 Cov.: 30 AF XY: 0.396 AC XY: 29407 AN XY: 74182

African (AFR) AF: 0.474 AC: 19594 AN: 41358

American (AMR) AF: 0.377 AC: 5749 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1023 AN: 3472

East Asian (EAS) AF: 0.654 AC: 3363 AN: 5144

South Asian (SAS) AF: 0.493 AC: 2379 AN: 4822

European-Finnish (FIN) AF: 0.353 AC: 3720 AN: 10534

Middle Eastern (MID) AF: 0.307 AC: 89 AN: 290

European-Non Finnish (NFE) AF: 0.332 AC: 22516 AN: 67916

Other (OTH) AF: 0.368 AC: 776 AN: 2106

Alfa AF: 0.353 Hom.: 5775

Bravo AF: 0.400

Asia WGS AF: 0.536 AC: 1860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.74
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs732102; hg19: chr10-97192545;