rs1007264

chr10-17668275-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003473.4(STAM):c.125+7727G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,140 control chromosomes in the GnomAD database, including 1,346 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 0.13 (1346 hom., cov: 32)
• Consequence: STAM NM_003473.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAM	NM_003473.4	c.125+7727G>A		intron_variant		ENST00000377524.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAM	ENST00000377524.8	c.125+7727G>A		intron_variant		1	NM_003473.4	P1
STAM	ENST00000377500.1	c.-36-19752G>A		intron_variant		5
STAM	ENST00000445846.1	c.126-4700G>A		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19026 AN: 152022 Hom.: 1343 Cov.: 32

Gnomad AFR AF: 0.161

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.174

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.0856

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0868

Gnomad OTH AF: 0.112

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.125 AC: 19047 AN: 152140 Hom.: 1346 Cov.: 32 AF XY: 0.128 AC XY: 9543 AN XY: 74398

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.174

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.0856

Gnomad4 NFE AF: 0.0868

Gnomad4 OTH AF: 0.114

Alfa AF: 0.106 Hom.: 167

Bravo AF: 0.135

Asia WGS AF: 0.218 AC: 758 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
Cadd	Benign	14
Dann	Benign	0.80

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

Other links and lift over

dbSNP: rs1007264; hg19: chr10-17710274;