dbSNP rs12221: STAM:p.Tyr480Tyr (chr10-17714597-T-C) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -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

Publications

18 publications found

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:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
STAM	NM_003473.4 link	c.1440T>C	p.Tyr480Tyr	synonymous_variant	Exon 14 of 14	ENST00000377524.8	NP_003464.1	Q92783-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAM	ENST00000377524.8 link	c.1440T>C	p.Tyr480Tyr	synonymous_variant	Exon 14 of 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

GnomAD2 exomes

AF:

0.193

AC:

48543

AN:

251368

AF XY:

0.194

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 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

African (AFR)

AF:

0.105

AC:

3527

AN:

33478

American (AMR)

AF:

0.112

AC:

5029

AN:

44724

Ashkenazi Jewish (ASJ)

AF:

0.270

AC:

7044

AN:

26136

East Asian (EAS)

AF:

0.204

AC:

8087

AN:

39700

South Asian (SAS)

AF:

0.138

AC:

11929

AN:

86258

European-Finnish (FIN)

AF:

0.254

AC:

13581

AN:

53410

Middle Eastern (MID)

AF:

0.251

AC:

1449

AN:

5768

European-Non Finnish (NFE)

AF:

0.220

AC:

245125

AN:

1111974

Other (OTH)

AF:

0.212

AC:

12833

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

14779

29557

44336

59114

73893

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8328

16656

24984

33312

41640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.183

AC:

27783

AN:

152152

Hom.:

2828

Cov.:

AF XY:

0.182

AC XY:

13558

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.104

AC:

4333

AN:

41512

American (AMR)

AF:

0.147

AC:

2252

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

995

AN:

3472

East Asian (EAS)

AF:

0.200

AC:

1034

AN:

5174

South Asian (SAS)

AF:

0.131

AC:

631

AN:

4818

European-Finnish (FIN)

AF:

0.257

AC:

2715

AN:

10580

Middle Eastern (MID)

AF:

0.204

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.223

AC:

15191

AN:

67994

Other (OTH)

AF:

0.207

AC:

438

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1161

2322

3484

4645

5806

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.212

Hom.:

15558

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

(source)

DANN

Benign

0.31

PhyloP100

-0.73

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

Mutation Taster

=98/2

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over