Variant rs12221 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_003473.4(STAM):c.1440T>C(p.Tyr480Tyr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,613,996 control chromosomes in the GnomAD database, including 36,514 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 0.18 ( 2828 hom., cov: 31)

Exomes 𝑓: 0.21 ( 33686 hom. )

Consequence

STAM
NM_003473.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.730

Variant links:

Genes affected

STAM (HGNC:11357): (signal transducing adaptor molecule) This gene encodes a member of the signal-transducing adaptor molecule family. These proteins mediate downstream signaling of cytokine receptors and also play a role in ER to Golgi trafficking by interacting with the coat protein II complex. The encoded protein also associates with hepatocyte growth factor-regulated substrate to form the endosomal sorting complex required for transport-0 (ESCRT-0), which sorts ubiquitinated membrane proteins to the ESCRT-1 complex for lysosomal degradation. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Feb 2011]

STAM links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.65).

BP7

Synonymous conserved (PhyloP=-0.73 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
STAM	NM_003473.4 linkuse as main transcript	c.1440T>C	p.Tyr480Tyr	synonymous_variant	14/14	ENST00000377524.8	NP_003464.1	Q92783-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STAM	ENST00000377524.8 linkuse as main transcript	c.1440T>C	p.Tyr480Tyr	synonymous_variant	14/14	1	NM_003473.4	ENSP00000366746.3		Q92783-1

Frequencies

GnomAD3 genomes

AF:

0.183

AC:

27772

AN:

152034

Hom.:

2824

Cov.:

show subpopulations

Gnomad AFR

AF:

0.104

Gnomad AMI

AF:

0.147

Gnomad AMR

AF:

0.148

Gnomad ASJ

AF:

0.287

Gnomad EAS

AF:

0.200

Gnomad SAS

AF:

0.131

Gnomad FIN

AF:

0.257

Gnomad MID

AF:

0.212

Gnomad NFE

AF:

0.223

Gnomad OTH

AF:

0.203

GnomAD3 exomes

AF:

0.193

AC:

48543

AN:

251368

Hom.:

5165

AF XY:

0.194

AC XY:

26379

AN XY:

135860

show subpopulations

Gnomad AFR exome

AF:

0.106

Gnomad AMR exome

AF:

0.107

Gnomad ASJ exome

AF:

0.268

Gnomad EAS exome

AF:

0.215

Gnomad SAS exome

AF:

0.133

Gnomad FIN exome

AF:

0.259

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.209

GnomAD4 exome

AF:

0.211

AC:

308604

AN:

1461844

Hom.:

33686

Cov.:

AF XY:

0.209

AC XY:

152225

AN XY:

727216

show subpopulations

Gnomad4 AFR exome

AF:

0.105

Gnomad4 AMR exome

AF:

0.112

Gnomad4 ASJ exome

AF:

0.270

Gnomad4 EAS exome

AF:

0.204

Gnomad4 SAS exome

AF:

0.138

Gnomad4 FIN exome

AF:

0.254

Gnomad4 NFE exome

AF:

0.220

Gnomad4 OTH exome

AF:

0.212

GnomAD4 genome

AF:

0.183

AC:

27783

AN:

152152

Hom.:

2828

Cov.:

AF XY:

0.182

AC XY:

13558

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.104

Gnomad4 AMR

AF:

0.147

Gnomad4 ASJ

AF:

0.287

Gnomad4 EAS

AF:

0.200

Gnomad4 SAS

AF:

0.131

Gnomad4 FIN

AF:

0.257

Gnomad4 NFE

AF:

0.223

Gnomad4 OTH

AF:

0.207

Alfa

AF:

0.218

Hom.:

7742

Bravo

AF:

0.173

Asia WGS

AF:

0.162

AC:

564

AN:

3478

EpiCase

AF:

0.230

EpiControl

AF:

0.229

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

0.11

DANN

Benign

0.31

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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