rs7340679

Positions:

• chr3-15305193-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000383791.8(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 ENST00000383791.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SH3BP5	NM_004844.5	c.202-962G>A		intron_variant		ENST00000383791.8	NP_004835.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SH3BP5	ENST00000383791.8	c.202-962G>A		intron_variant		1	NM_004844.5	ENSP00000373301	P1

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

Gnomad4 AFR AF: 0.967

Gnomad4 AMR AF: 0.908

Gnomad4 ASJ AF: 0.868

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.964

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.814

Gnomad4 OTH AF: 0.896

Alfa AF: 0.835 Hom.: 32078

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

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

Other links and lift over

dbSNP: rs7340679; hg19: chr3-15346700;