10-17668275-G-A

Variant names:

• chr10-17668275-G-A
• rs1007264
• NM_003473.4:c.125+7727G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003473.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAM	NM_003473.4	MANE Select	c.125+7727G>A		intron	N/A	NP_003464.1
	STAM	NM_001324282.2		c.125+7727G>A		intron	N/A	NP_001311211.1
	STAM	NM_001324283.2		c.-25-16400G>A		intron	N/A	NP_001311212.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STAM	ENST00000377524.8	TSL:1 MANE Select	c.125+7727G>A		intron	N/A	ENSP00000366746.3
	STAM	ENST00000377500.1	TSL:5	c.-36-19752G>A		intron	N/A	ENSP00000366721.1
	STAM	ENST00000445846.1	TSL:4	n.126-4700G>A		intron	N/A	ENSP00000400025.1

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

African (AFR) AF: 0.161 AC: 6695 AN: 41488

American (AMR) AF: 0.174 AC: 2662 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0984 AC: 341 AN: 3466

East Asian (EAS) AF: 0.259 AC: 1341 AN: 5178

South Asian (SAS) AF: 0.185 AC: 892 AN: 4816

European-Finnish (FIN) AF: 0.0856 AC: 906 AN: 10590

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0868 AC: 5905 AN: 68008

Other (OTH) AF: 0.114 AC: 240 AN: 2112

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.80
PhyloP100		1.0
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1007264; hg19: chr10-17710274;