Variant rs2008734 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_021200.3(PLEKHB1):c.391-151G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 632,112 control chromosomes in the GnomAD database, including 87,847 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 0.48 ( 18779 hom., cov: 32)

Exomes 𝑓: 0.53 ( 69068 hom. )

Consequence

PLEKHB1
NM_021200.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.831

Variant links:

Genes affected

PLEKHB1 (HGNC:19079): (pleckstrin homology domain containing B1) Predicted to enable protein C-terminus binding activity and protein homodimerization activity. Predicted to be involved in regulation of cell differentiation. Is integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

PLEKHB1 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=-0.62).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.562 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PLEKHB1	NM_021200.3 linkuse as main transcript	c.391-151G>A		intron_variant		ENST00000354190.10	NP_067023.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PLEKHB1	ENST00000354190.10 linkuse as main transcript	c.391-151G>A		intron_variant		1	NM_021200.3	ENSP00000346127		Q9UF11-1

Frequencies

GnomAD3 genomes

AF:

0.482

AC:

73201

AN:

151934

Hom.:

18770

Cov.:

show subpopulations

Gnomad AFR

AF:

0.299

Gnomad AMI

AF:

0.633

Gnomad AMR

AF:

0.540

Gnomad ASJ

AF:

0.547

Gnomad EAS

AF:

0.507

Gnomad SAS

AF:

0.401

Gnomad FIN

AF:

0.559

Gnomad MID

AF:

0.510

Gnomad NFE

AF:

0.566

Gnomad OTH

AF:

0.493

GnomAD4 exome

AF:

0.530

AC:

254533

AN:

480058

Hom.:

69068

AF XY:

0.523

AC XY:

131994

AN XY:

252142

show subpopulations

Gnomad4 AFR exome

AF:

0.297

Gnomad4 AMR exome

AF:

0.554

Gnomad4 ASJ exome

AF:

0.534

Gnomad4 EAS exome

AF:

0.479

Gnomad4 SAS exome

AF:

0.403

Gnomad4 FIN exome

AF:

0.550

Gnomad4 NFE exome

AF:

0.565

Gnomad4 OTH exome

AF:

0.524

GnomAD4 genome

AF:

0.482

AC:

73238

AN:

152054

Hom.:

18779

Cov.:

AF XY:

0.482

AC XY:

35797

AN XY:

74312

show subpopulations

Gnomad4 AFR

AF:

0.298

Gnomad4 AMR

AF:

0.540

Gnomad4 ASJ

AF:

0.547

Gnomad4 EAS

AF:

0.506

Gnomad4 SAS

AF:

0.402

Gnomad4 FIN

AF:

0.559

Gnomad4 NFE

AF:

0.566

Gnomad4 OTH

AF:

0.495

Alfa

AF:

0.511

Hom.:

3682

Bravo

AF:

0.476

Asia WGS

AF:

0.432

AC:

1503

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.62

CADD

Benign

DANN

Benign

0.84

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