Variant rs393569 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_138392.4(SHKBP1):c.1493-150A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 1,264,686 control chromosomes in the GnomAD database, including 168,242 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 0.58 ( 26619 hom., cov: 31)

Exomes 𝑓: 0.50 ( 141623 hom. )

Consequence

SHKBP1
NM_138392.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.654

Variant links:

Genes affected

SHKBP1 (HGNC:19214): (SH3KBP1 binding protein 1) Enables identical protein binding activity. Predicted to be involved in positive regulation of epidermal growth factor receptor signaling pathway. Predicted to be located in lysosome. [provided by Alliance of Genome Resources, Apr 2022]

SHKBP1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.772 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SHKBP1	NM_138392.4 linkuse as main transcript	c.1493-150A>G		intron_variant		ENST00000291842.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SHKBP1	ENST00000291842.10 linkuse as main transcript	c.1493-150A>G		intron_variant		1	NM_138392.4	P1	Q8TBC3-1

Frequencies

GnomAD3 genomes

AF:

0.577

AC:

87575

AN:

151848

Hom.:

26568

Cov.:

show subpopulations

Gnomad AFR

AF:

0.779

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.523

Gnomad ASJ

AF:

0.607

Gnomad EAS

AF:

0.405

Gnomad SAS

AF:

0.552

Gnomad FIN

AF:

0.539

Gnomad MID

AF:

0.513

Gnomad NFE

AF:

0.489

Gnomad OTH

AF:

0.538

GnomAD4 exome

AF:

0.499

AC:

555763

AN:

1112720

Hom.:

141623

Cov.:

AF XY:

0.501

AC XY:

277793

AN XY:

554348

show subpopulations

Gnomad4 AFR exome

AF:

0.794

Gnomad4 AMR exome

AF:

0.533

Gnomad4 ASJ exome

AF:

0.598

Gnomad4 EAS exome

AF:

0.374

Gnomad4 SAS exome

AF:

0.555

Gnomad4 FIN exome

AF:

0.527

Gnomad4 NFE exome

AF:

0.484

Gnomad4 OTH exome

AF:

0.530

GnomAD4 genome

AF:

0.577

AC:

87689

AN:

151966

Hom.:

26619

Cov.:

AF XY:

0.577

AC XY:

42886

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.779

Gnomad4 AMR

AF:

0.523

Gnomad4 ASJ

AF:

0.607

Gnomad4 EAS

AF:

0.404

Gnomad4 SAS

AF:

0.554

Gnomad4 FIN

AF:

0.539

Gnomad4 NFE

AF:

0.489

Gnomad4 OTH

AF:

0.537

Alfa

AF:

0.504

Hom.:

31617

Bravo

AF:

0.586

Asia WGS

AF:

0.514

AC:

1788

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

1.4

DANN

Benign

0.49

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over