rs9310472

Positions:

• chr3-15265092-C-T

Variant summary

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

The NM_004844.5(SH3BP5):​c.496-2803G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 151,942 control chromosomes in the GnomAD database, including 555 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 0.056 (555 hom., cov: 31)
• Consequence: SH3BP5 NM_004844.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.203

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=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.144 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SH3BP5	NM_004844.5	c.496-2803G>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.496-2803G>A		intron_variant		1	NM_004844.5	ENSP00000373301.3

Frequencies

GnomAD3 genomes AF: 0.0556 AC: 8439 AN: 151824 Hom.: 548 Cov.: 31

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.0285

Gnomad AMR AF: 0.0251

Gnomad ASJ AF: 0.00404

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0668

Gnomad FIN AF: 0.00850

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0137

Gnomad OTH AF: 0.0379

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

GnomAD4 genome AF: 0.0558 AC: 8472 AN: 151942 Hom.: 555 Cov.: 31 AF XY: 0.0552 AC XY: 4099 AN XY: 74272

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.0250

Gnomad4 ASJ AF: 0.00404

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.00850

Gnomad4 NFE AF: 0.0137

Gnomad4 OTH AF: 0.0389

Alfa AF: 0.0336 Hom.: 66

Bravo AF: 0.0608

Asia WGS AF: 0.0850 AC: 295 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.7
DANN	Benign	0.35

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: rs9310472; hg19: chr3-15306599;