Variant X-19541911-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_031892.3(SH3KBP1):c.1892+14G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00622 in 1,196,833 control chromosomes in the GnomAD database, including 173 homozygotes. There are 2,358 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.025 ( 87 hom., 763 hem., cov: 22)

Exomes 𝑓: 0.0043 ( 86 hom. 1595 hem. )

Consequence

SH3KBP1
NM_031892.3 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.29

Variant links:

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]

SH3KBP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant X-19541911-C-T is Benign according to our data. Variant chrX-19541911-C-T is described in ClinVar as [Benign]. Clinvar id is 1167394.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH3KBP1	NM_031892.3 linkuse as main transcript	c.1892+14G>A		intron_variant		ENST00000397821.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH3KBP1	ENST00000397821.8 linkuse as main transcript	c.1892+14G>A		intron_variant		1	NM_031892.3	P2	Q96B97-1

Frequencies

GnomAD3 genomes

AF:

0.0253

AC:

2821

AN:

111654

Hom.:

Cov.:

AF XY:

0.0226

AC XY:

763

AN XY:

33832

show subpopulations

Gnomad AFR

AF:

0.0852

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00857

Gnomad ASJ

AF:

0.00226

Gnomad EAS

AF:

0.00450

Gnomad SAS

AF:

0.0155

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00420

Gnomad NFE

AF:

0.000527

Gnomad OTH

AF:

0.0192

GnomAD3 exomes

AF:

0.00999

AC:

1672

AN:

167393

Hom.:

AF XY:

0.00828

AC XY:

453

AN XY:

54689

show subpopulations

Gnomad AFR exome

AF:

0.0854

Gnomad AMR exome

AF:

0.00610

Gnomad ASJ exome

AF:

0.00403

Gnomad EAS exome

AF:

0.00218

Gnomad SAS exome

AF:

0.0203

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000296

Gnomad OTH exome

AF:

0.00511

GnomAD4 exome

AF:

0.00426

AC:

4620

AN:

1085127

Hom.:

Cov.:

AF XY:

0.00451

AC XY:

1595

AN XY:

353567

show subpopulations

Gnomad4 AFR exome

AF:

0.0866

Gnomad4 AMR exome

AF:

0.00640

Gnomad4 ASJ exome

AF:

0.00393

Gnomad4 EAS exome

AF:

0.0168

Gnomad4 SAS exome

AF:

0.0208

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000132

Gnomad4 OTH exome

AF:

0.00760

GnomAD4 genome

AF:

0.0253

AC:

2822

AN:

111706

Hom.:

Cov.:

AF XY:

0.0225

AC XY:

763

AN XY:

33894

show subpopulations

Gnomad4 AFR

AF:

0.0851

Gnomad4 AMR

AF:

0.00856

Gnomad4 ASJ

AF:

0.00226

Gnomad4 EAS

AF:

0.00452

Gnomad4 SAS

AF:

0.0151

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000528

Gnomad4 OTH

AF:

0.0190

Alfa

AF:

0.00634

Hom.:

167

Bravo

AF:

0.0288

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

4.3

DANN

Benign

0.28

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over