Variant rs12254856 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.587G>A(p.Ser196Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 1,613,812 control chromosomes in the GnomAD database, including 16,044 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict 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 same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.13 ( 1420 hom., cov: 32)

Exomes 𝑓: 0.14 ( 14624 hom. )

Consequence

STAMBPL1
NM_020799.4 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.34

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:

STAMBPL1 (HGNC:):

STAMBPL1 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 (MetaRNN=0.0011698604).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.151 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAMBPL1	NM_020799.4 linkuse as main transcript	c.587G>A	p.Ser196Asn	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 linkuse as main transcript	c.587G>A	p.Ser196Asn	missense_variant	6/11	1	NM_020799.4	ENSP00000360994.3	Q96FJ0-1
STAMBPL1	ENST00000371924.5 linkuse as main transcript	c.587G>A	p.Ser196Asn	missense_variant	5/10	1		ENSP00000360992.1	Q96FJ0-1
STAMBPL1	ENST00000371927.7 linkuse as main transcript	c.587G>A	p.Ser196Asn	missense_variant	6/11	2		ENSP00000360995.3	Q96FJ0-2
STAMBPL1	ENST00000371922.1 linkuse as main transcript	n.912G>A		non_coding_transcript_exon_variant	1/6	2

Frequencies

GnomAD3 genomes

AF:

0.129

AC:

19670

AN:

152114

Hom.:

1417

Cov.:

show subpopulations

Gnomad AFR

AF:

0.154

Gnomad AMI

AF:

0.0866

Gnomad AMR

AF:

0.111

Gnomad ASJ

AF:

0.0840

Gnomad EAS

AF:

0.00211

Gnomad SAS

AF:

0.0722

Gnomad FIN

AF:

0.0738

Gnomad MID

AF:

0.0570

Gnomad NFE

AF:

0.145

Gnomad OTH

AF:

0.103

GnomAD3 exomes

AF:

0.108

AC:

26962

AN:

250718

Hom.:

1702

AF XY:

0.107

AC XY:

14494

AN XY:

135472

show subpopulations

Gnomad AFR exome

AF:

0.154

Gnomad AMR exome

AF:

0.0824

Gnomad ASJ exome

AF:

0.0875

Gnomad EAS exome

AF:

0.00142

Gnomad SAS exome

AF:

0.0714

Gnomad FIN exome

AF:

0.0719

Gnomad NFE exome

AF:

0.144

Gnomad OTH exome

AF:

0.111

GnomAD4 exome

AF:

0.137

AC:

199841

AN:

1461580

Hom.:

14624

Cov.:

AF XY:

0.135

AC XY:

97897

AN XY:

727094

show subpopulations

Gnomad4 AFR exome

AF:

0.155

Gnomad4 AMR exome

AF:

0.0859

Gnomad4 ASJ exome

AF:

0.0875

Gnomad4 EAS exome

AF:

0.000605

Gnomad4 SAS exome

AF:

0.0745

Gnomad4 FIN exome

AF:

0.0785

Gnomad4 NFE exome

AF:

0.152

Gnomad4 OTH exome

AF:

0.130

GnomAD4 genome

AF:

0.129

AC:

19688

AN:

152232

Hom.:

1420

Cov.:

AF XY:

0.123

AC XY:

9183

AN XY:

74432

show subpopulations

Gnomad4 AFR

AF:

0.154

Gnomad4 AMR

AF:

0.111

Gnomad4 ASJ

AF:

0.0840

Gnomad4 EAS

AF:

0.00212

Gnomad4 SAS

AF:

0.0714

Gnomad4 FIN

AF:

0.0738

Gnomad4 NFE

AF:

0.145

Gnomad4 OTH

AF:

0.102

Alfa

AF:

0.138

Hom.:

3834

Bravo

AF:

0.133

ESP6500AA

AF:

0.160

AC:

705

ESP6500EA

AF:

0.143

AC:

1228

ExAC

AF:

0.111

AC:

13479

Asia WGS

AF:

0.0410

AC:

144

AN:

3478

EpiCase

AF:

0.146

EpiControl

AF:

0.141

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.065

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

DANN

Benign

0.93

DEOGEN2

Benign

0.0045

T;.;T;.

Eigen

Benign

-0.91

Eigen_PC

Benign

-0.76

FATHMM_MKL

Benign

0.22

LIST_S2

Benign

0.59

T;T;.;T

MetaRNN

Benign

0.0012

T;T;T;T

MetaSVM

Benign

-0.98

MutationAssessor

Benign

0.71

N;N;N;.

PrimateAI

Benign

0.31

PROVEAN

Benign

-1.0

N;N;N;N

REVEL

Benign

0.11

Sift

Benign

0.49

T;T;T;T

Sift4G

Benign

0.51

T;T;T;T

Polyphen

0.0

B;B;B;.

Vest4

0.029

MPC

0.066

ClinPred

0.0017

GERP RS

3.9

Varity_R

0.042

gMVP

0.28

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.040

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