Genetic Variant STAM:c.1385+96T>C (chr10-17709047-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_003473.4(STAM):c.1385+96T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0881 in 1,435,320 control chromosomes in the GnomAD database, including 5,876 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 0.086 ( 599 hom., cov: 32)

Exomes 𝑓: 0.088 ( 5277 hom. )

Consequence

STAM
NM_003473.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.165

Publications

3 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAM	NM_003473.4 link	c.1385+96T>C		intron_variant	Intron 13 of 13	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.1385+96T>C		intron_variant	Intron 13 of 13	1	NM_003473.4	ENSP00000366746.3		Q92783-1

Frequencies

GnomAD3 genomes

AF:

0.0860

AC:

13075

AN:

152120

Hom.:

598

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0652

Gnomad AMI

AF:

0.118

Gnomad AMR

AF:

0.117

Gnomad ASJ

AF:

0.0686

Gnomad EAS

AF:

0.0517

Gnomad SAS

AF:

0.0701

Gnomad FIN

AF:

0.0849

Gnomad MID

AF:

0.108

Gnomad NFE

AF:

0.0961

Gnomad OTH

AF:

0.0781

GnomAD4 exome

AF:

0.0883

AC:

113321

AN:

1283082

Hom.:

5277

AF XY:

0.0877

AC XY:

55439

AN XY:

632154

show subpopulations

African (AFR)

AF:

0.0649

AC:

1874

AN:

28884

American (AMR)

AF:

0.111

AC:

3672

AN:

33206

Ashkenazi Jewish (ASJ)

AF:

0.0682

AC:

1361

AN:

19960

East Asian (EAS)

AF:

0.0426

AC:

1613

AN:

37892

South Asian (SAS)

AF:

0.0611

AC:

4293

AN:

70214

European-Finnish (FIN)

AF:

0.0888

AC:

4323

AN:

48670

Middle Eastern (MID)

AF:

0.0961

AC:

478

AN:

4972

European-Non Finnish (NFE)

AF:

0.0924

AC:

91072

AN:

985816

Other (OTH)

AF:

0.0867

AC:

4635

AN:

53468

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

4867

9734

14601

19468

24335

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

3322

6644

9966

13288

16610

<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:

0.0860

AC:

13087

AN:

152238

Hom.:

599

Cov.:

AF XY:

0.0856

AC XY:

6374

AN XY:

74440

show subpopulations

African (AFR)

AF:

0.0652

AC:

2706

AN:

41528

American (AMR)

AF:

0.118

AC:

1798

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.0686

AC:

238

AN:

3470

East Asian (EAS)

AF:

0.0520

AC:

270

AN:

5190

South Asian (SAS)

AF:

0.0699

AC:

337

AN:

4820

European-Finnish (FIN)

AF:

0.0849

AC:

901

AN:

10608

Middle Eastern (MID)

AF:

0.102

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0961

AC:

6536

AN:

68010

Other (OTH)

AF:

0.0773

AC:

163

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

613

1226

1840

2453

3066

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

144

288

432

576

720

<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:

0.0882

Hom.:

161

Bravo

AF:

0.0861

Asia WGS

AF:

0.0800

AC:

279

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

5.7

(source)

DANN

Benign

0.50

PhyloP100

-0.17

Mutation Taster

=100/0

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