rs164124

Variant names:

• chr1-162397445-G-A
• rs164124
• NM_053282.5:c.364-130C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-162397445-G-A
• chr1-162397445-G-T

Variant summary

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

The NM_053282.5(SH2D1B):​c.364-130C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.65 in 905,384 control chromosomes in the GnomAD database, including 195,613 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 0.59 (27648 hom., cov: 31)
  • Exomes 𝑓: 0.66 (167965 hom.)
• Consequence: SH2D1B NM_053282.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 8 publications found

Genes affected

SH2D1B (HGNC:30416): (SH2 domain containing 1B) By binding phosphotyrosines through its free SRC (MIM 190090) homology-2 (SH2) domain, EAT2 regulates signal transduction through receptors expressed on the surface of antigen-presenting cells (Morra et al., 2001 [PubMed 11689425]).[supplied by OMIM, Mar 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.729 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH2D1B	NM_053282.5	c.364-130C>T		intron_variant	Intron 3 of 3	ENST00000367929.3	NP_444512.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH2D1B	ENST00000367929.3	c.364-130C>T		intron_variant	Intron 3 of 3	1	NM_053282.5	ENSP00000356906.2

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88929 AN: 151804 Hom.: 27635 Cov.: 31

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.697

Gnomad ASJ AF: 0.696

Gnomad EAS AF: 0.749

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.595

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.675

Gnomad OTH AF: 0.626

GnomAD4 exome AF: 0.664 AC: 499927 AN: 753462 Hom.: 167965 AF XY: 0.665 AC XY: 262878 AN XY: 395116

African (AFR) AF: 0.353 AC: 6575 AN: 18640

American (AMR) AF: 0.708 AC: 21378 AN: 30214

Ashkenazi Jewish (ASJ) AF: 0.702 AC: 13339 AN: 18992

East Asian (EAS) AF: 0.717 AC: 24698 AN: 34442

South Asian (SAS) AF: 0.665 AC: 41788 AN: 62840

European-Finnish (FIN) AF: 0.611 AC: 22610 AN: 36982

Middle Eastern (MID) AF: 0.731 AC: 3115 AN: 4264

European-Non Finnish (NFE) AF: 0.671 AC: 342653 AN: 510880

Other (OTH) AF: 0.657 AC: 23771 AN: 36208

GnomAD4 genome AF: 0.586 AC: 88976 AN: 151922 Hom.: 27648 Cov.: 31 AF XY: 0.588 AC XY: 43633 AN XY: 74252

African (AFR) AF: 0.354 AC: 14649 AN: 41414

American (AMR) AF: 0.697 AC: 10638 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.696 AC: 2412 AN: 3464

East Asian (EAS) AF: 0.748 AC: 3873 AN: 5176

South Asian (SAS) AF: 0.660 AC: 3166 AN: 4800

European-Finnish (FIN) AF: 0.595 AC: 6287 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.675 AC: 45831 AN: 67934

Other (OTH) AF: 0.623 AC: 1311 AN: 2104

Alfa AF: 0.653 Hom.: 42071

Bravo AF: 0.581

Asia WGS AF: 0.696 AC: 2420 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	0.78
DANN	Benign	0.30
PhyloP100		0.11
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: rs164124; hg19: chr1-162367235; COSMIC: COSV63392075;