Variant chr2-73830868-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_213622.4(STAMBP):c.12T>C(p.His4=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0353 in 1,612,874 control chromosomes in the GnomAD database, including 3,548 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.096 ( 1566 hom., cov: 32)

Exomes 𝑓: 0.029 ( 1982 hom. )

Consequence

STAMBP
NM_213622.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 1.97

Variant links:

Genes affected

STAMBP (HGNC:16950): (STAM binding protein) Cytokine-mediated signal transduction in the JAK-STAT cascade requires the involvement of adaptor molecules. One such signal-transducing adaptor molecule contains an SH3 domain that is required for induction of MYC and cell growth. The protein encoded by this gene binds to the SH3 domain of the signal-transducing adaptor molecule, and plays a critical role in cytokine-mediated signaling for MYC induction and cell cycle progression. Multiple alternatively spliced transcript variants encoding the same protein isoform have been found for this gene. [provided by RefSeq, Jul 2008]

STAMBP links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.61).

BP6

Variant 2-73830868-T-C is Benign according to our data. Variant chr2-73830868-T-C is described in ClinVar as [Benign]. Clinvar id is 160044.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr2-73830868-T-C is described in Lovd as [Benign].

BP7

Synonymous conserved (PhyloP=1.97 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAMBP	NM_213622.4 linkuse as main transcript	c.12T>C	p.His4=	synonymous_variant	2/10	ENST00000394070.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAMBP	ENST00000394070.7 linkuse as main transcript	c.12T>C	p.His4=	synonymous_variant	2/10	1	NM_213622.4	P4	O95630-1

Frequencies

GnomAD3 genomes

AF:

0.0954

AC:

14515

AN:

152160

Hom.:

1550

Cov.:

show subpopulations

Gnomad AFR

AF:

0.263

Gnomad AMI

AF:

0.00220

Gnomad AMR

AF:

0.0969

Gnomad ASJ

AF:

0.0617

Gnomad EAS

AF:

0.0528

Gnomad SAS

AF:

0.0255

Gnomad FIN

AF:

0.0224

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0164

Gnomad OTH

AF:

0.0818

GnomAD3 exomes

AF:

0.0541

AC:

13571

AN:

250954

Hom.:

942

AF XY:

0.0458

AC XY:

6210

AN XY:

135672

show subpopulations

Gnomad AFR exome

AF:

0.271

Gnomad AMR exome

AF:

0.114

Gnomad ASJ exome

AF:

0.0635

Gnomad EAS exome

AF:

0.0530

Gnomad SAS exome

AF:

0.0253

Gnomad FIN exome

AF:

0.0271

Gnomad NFE exome

AF:

0.0176

Gnomad OTH exome

AF:

0.0423

GnomAD4 exome

AF:

0.0290

AC:

42286

AN:

1460596

Hom.:

1982

Cov.:

AF XY:

0.0277

AC XY:

20111

AN XY:

726614

show subpopulations

Gnomad4 AFR exome

AF:

0.272

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.0627

Gnomad4 EAS exome

AF:

0.0538

Gnomad4 SAS exome

AF:

0.0251

Gnomad4 FIN exome

AF:

0.0254

Gnomad4 NFE exome

AF:

0.0163

Gnomad4 OTH exome

AF:

0.0398

GnomAD4 genome

AF:

0.0957

AC:

14580

AN:

152278

Hom.:

1566

Cov.:

AF XY:

0.0940

AC XY:

7000

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.263

Gnomad4 AMR

AF:

0.0969

Gnomad4 ASJ

AF:

0.0617

Gnomad4 EAS

AF:

0.0534

Gnomad4 SAS

AF:

0.0251

Gnomad4 FIN

AF:

0.0224

Gnomad4 NFE

AF:

0.0164

Gnomad4 OTH

AF:

0.0814

Alfa

AF:

0.0376

Hom.:

221

Bravo

AF:

0.111

Asia WGS

AF:

0.0580

AC:

203

AN:

3478

EpiCase

AF:

0.0209

EpiControl

AF:

0.0210

ClinVar

Significance: Benign

Submissions summary: Benign:7

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:3

Benign, no assertion criteria provided	clinical testing	Clinical Genetics, Academic Medical Center	-	- -
Likely benign, no assertion criteria provided	clinical testing	Genetic Services Laboratory, University of Chicago	-	- -
Benign, no assertion criteria provided	clinical testing	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	-	- -

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2018	- -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -

Microcephaly-capillary malformation syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Jul 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.61

CADD

Benign

DANN

Benign

0.81

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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