rs7340679

Variant names:

• chr3-15305193-C-T
• rs7340679
• NM_004844.5:c.202-962G>A

Variant summary

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

The NM_004844.5(SH3BP5):​c.202-962G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,136 control chromosomes in the GnomAD database, including 59,213 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 0.88 (59213 hom., cov: 31)
• Consequence: SH3BP5 NM_004844.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 2 publications found

Genes affected

SH3BP5 (HGNC:10827): (SH3 domain binding protein 5) Enables guanyl-nucleotide exchange factor activity and protein kinase inhibitor activity. Acts upstream of or within intracellular signal transduction. Located in cytoplasmic vesicle membrane and nuclear body. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.977 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH3BP5	NM_004844.5	c.202-962G>A		intron_variant	Intron 2 of 8	ENST00000383791.8	NP_004835.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH3BP5	ENST00000383791.8	c.202-962G>A		intron_variant	Intron 2 of 8	1	NM_004844.5	ENSP00000373301.3

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133598 AN: 152018 Hom.: 59149 Cov.: 31

Gnomad AFR AF: 0.967

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.908

Gnomad ASJ AF: 0.868

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.964

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.814

Gnomad OTH AF: 0.894

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

GnomAD4 genome AF: 0.879 AC: 133722 AN: 152136 Hom.: 59213 Cov.: 31 AF XY: 0.882 AC XY: 65559 AN XY: 74356

African (AFR) AF: 0.967 AC: 40104 AN: 41468

American (AMR) AF: 0.908 AC: 13899 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.868 AC: 3015 AN: 3472

East Asian (EAS) AF: 0.999 AC: 5182 AN: 5186

South Asian (SAS) AF: 0.964 AC: 4648 AN: 4822

European-Finnish (FIN) AF: 0.818 AC: 8626 AN: 10550

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.814 AC: 55343 AN: 68022

Other (OTH) AF: 0.896 AC: 1890 AN: 2110

Alfa AF: 0.836 Hom.: 35099

Bravo AF: 0.889

Asia WGS AF: 0.977 AC: 3397 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	0.21
DANN	Benign	0.36
PhyloP100		-1.3
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: rs7340679; hg19: chr3-15346700;