rs1017874

chrX-19851528-G-A

Variant summary

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

The NM_031892.3(SH3KBP1):c.5-15246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 111,005 control chromosomes in the GnomAD database, including 4,035 homozygotes. There are 7,934 hemizygotes in GnomAD. 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 0.25 (4035 hom., 7934 hem., cov: 23)
• Consequence: SH3KBP1 NM_031892.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.15

Genes affected

SH3KBP1 (HGNC:13867): (SH3 domain containing kinase binding protein 1) This gene encodes an adapter protein that contains one or more N-terminal Src homology domains, a proline rich region and a C-terminal coiled-coil domain. The encoded protein facilitates protein-protein interactions and has been implicated in numerous cellular processes including apoptosis, cytoskeletal rearrangement, cell adhesion and in the regulation of clathrin-dependent endocytosis. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2017]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH3KBP1	NM_031892.3	c.5-15246C>T		intron_variant		ENST00000397821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH3KBP1	ENST00000397821.8	c.5-15246C>T		intron_variant		1	NM_031892.3	P2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 28089 AN: 110953 Hom.: 4033 Cov.: 23 AF XY: 0.238 AC XY: 7896 AN XY: 33203

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0155

Gnomad SAS AF: 0.0460

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.253 AC: 28137 AN: 111005 Hom.: 4035 Cov.: 23 AF XY: 0.239 AC XY: 7934 AN XY: 33265

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.110

Gnomad4 EAS AF: 0.0152

Gnomad4 SAS AF: 0.0466

Gnomad4 FIN AF: 0.241

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.244

Alfa AF: 0.155 Hom.: 8259

Bravo AF: 0.266

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.3
Dann	Benign	0.76

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: rs1017874; hg19: chrX-19869646;