Variant rs34270879 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_020799.4(STAMBPL1):c.610G>A(p.Glu204Lys) variant causes a missense change. The variant allele was found at a frequency of 0.0351 in 1,613,922 control chromosomes in the GnomAD database, including 1,164 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. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.

Frequency

Genomes: 𝑓 0.029 ( 91 hom., cov: 32)

Exomes 𝑓: 0.036 ( 1073 hom. )

Consequence

STAMBPL1
NM_020799.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.13

Variant links:

Genes affected

STAMBPL1 (HGNC:24105): (STAM binding protein like 1) Predicted to enable Lys63-specific deubiquitinase activity and thiol-dependent deubiquitinase. Predicted to be involved in protein K63-linked deubiquitination. Located in membrane. [provided by Alliance of Genome Resources, Apr 2022]

STAMBPL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0024805367).

BA1

GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0714 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAMBPL1	NM_020799.4 link	c.610G>A	p.Glu204Lys	missense_variant	6/11	ENST00000371926.8	NP_065850.1	Q96FJ0-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	UniProt
STAMBPL1	ENST00000371926.8 link	c.610G>A	p.Glu204Lys	missense_variant	6/11	1	NM_020799.4	ENSP00000360994.3	Q96FJ0-1
STAMBPL1	ENST00000371924.5 link	c.610G>A	p.Glu204Lys	missense_variant	5/10	1		ENSP00000360992.1	Q96FJ0-1
STAMBPL1	ENST00000371927.7 link	c.610G>A	p.Glu204Lys	missense_variant	6/11	2		ENSP00000360995.3	Q96FJ0-2
STAMBPL1	ENST00000371922.1 link	n.935G>A		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.0294

AC:

4475

AN:

152208

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00663

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.0310

Gnomad ASJ

AF:

0.0720

Gnomad EAS

AF:

0.000384

Gnomad SAS

AF:

0.0176

Gnomad FIN

AF:

0.0390

Gnomad MID

AF:

0.101

Gnomad NFE

AF:

0.0408

Gnomad OTH

AF:

0.0334

GnomAD3 exomes

AF:

0.0305

AC:

7647

AN:

250710

Hom.:

171

AF XY:

0.0315

AC XY:

4274

AN XY:

135506

show subpopulations

Gnomad AFR exome

AF:

0.00511

Gnomad AMR exome

AF:

0.0178

Gnomad ASJ exome

AF:

0.0701

Gnomad EAS exome

AF:

0.0000544

Gnomad SAS exome

AF:

0.0212

Gnomad FIN exome

AF:

0.0395

Gnomad NFE exome

AF:

0.0400

Gnomad OTH exome

AF:

0.0343

GnomAD4 exome

AF:

0.0357

AC:

52210

AN:

1461596

Hom.:

1073

Cov.:

AF XY:

0.0358

AC XY:

26027

AN XY:

727106

show subpopulations

Gnomad4 AFR exome

AF:

0.00658

Gnomad4 AMR exome

AF:

0.0187

Gnomad4 ASJ exome

AF:

0.0711

Gnomad4 EAS exome

AF:

0.0000504

Gnomad4 SAS exome

AF:

0.0210

Gnomad4 FIN exome

AF:

0.0401

Gnomad4 NFE exome

AF:

0.0383

Gnomad4 OTH exome

AF:

0.0376

GnomAD4 genome

AF:

0.0294

AC:

4475

AN:

152326

Hom.:

Cov.:

AF XY:

0.0288

AC XY:

2145

AN XY:

74492

show subpopulations

Gnomad4 AFR

AF:

0.00664

Gnomad4 AMR

AF:

0.0309

Gnomad4 ASJ

AF:

0.0720

Gnomad4 EAS

AF:

0.000385

Gnomad4 SAS

AF:

0.0180

Gnomad4 FIN

AF:

0.0390

Gnomad4 NFE

AF:

0.0407

Gnomad4 OTH

AF:

0.0331

Alfa

AF:

0.0391

Hom.:

215

Bravo

AF:

0.0278

TwinsUK

AF:

0.0415

AC:

154

ALSPAC

AF:

0.0330

AC:

127

ESP6500AA

AF:

0.00749

AC:

ESP6500EA

AF:

0.0429

AC:

369

ExAC

AF:

0.0298

AC:

3614

Asia WGS

AF:

0.0120

AC:

AN:

3478

EpiCase

AF:

0.0460

EpiControl

AF:

0.0466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.10

BayesDel_addAF

Benign

-0.46

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Pathogenic

1.0

DEOGEN2

Benign

0.0035

T;.;T;.

Eigen

Uncertain

0.27

Eigen_PC

Uncertain

0.40

FATHMM_MKL

Uncertain

0.94

LIST_S2

Uncertain

0.92

D;D;.;D

MetaRNN

Benign

0.0025

T;T;T;T

MetaSVM

Benign

-1.1

MutationAssessor

Uncertain

2.2

M;M;M;.

PrimateAI

Uncertain

0.51

PROVEAN

Benign

-1.1

N;N;N;N

REVEL

Benign

0.16

Sift

Benign

0.20

T;T;T;T

Sift4G

Benign

0.82

T;T;T;T

Polyphen

1.0

D;P;D;.

Vest4

0.36

MPC

0.44

ClinPred

0.028

GERP RS

6.0

Varity_R

0.082

gMVP

0.45

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