rs10930939

Variant names:

• chr2-152123419-C-T
• rs10930939
• NM_005843.6:c.1349+347G>A

Variant summary

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

The NM_005843.6(STAM2):​c.1349+347G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.284 in 151,982 control chromosomes in the GnomAD database, including 6,458 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 0.28 (6458 hom., cov: 32)
• Consequence: STAM2 NM_005843.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.381

Genes affected

STAM2 (HGNC:11358): (signal transducing adaptor molecule 2) The protein encoded by this gene is closely related to STAM, an adaptor protein involved in the downstream signaling of cytokine receptors, both of which contain a SH3 domain and the immunoreceptor tyrosine-based activation motif (ITAM). Similar to STAM, this protein acts downstream of JAK kinases, and is phosphorylated in response to cytokine stimulation. This protein and STAM thus are thought to exhibit compensatory effects on the signaling pathway downstream of JAK kinases upon cytokine stimulation. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STAM2	NM_005843.6	c.1349+347G>A		intron_variant	Intron 13 of 13	ENST00000263904.5	NP_005834.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STAM2	ENST00000263904.5	c.1349+347G>A		intron_variant	Intron 13 of 13	1	NM_005843.6	ENSP00000263904.4
STAM2	ENST00000489389.1	n.921+347G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.283 AC: 43013 AN: 151862 Hom.: 6433 Cov.: 32

Gnomad AFR AF: 0.374

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.264

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.194

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.284 AC: 43104 AN: 151982 Hom.: 6458 Cov.: 32 AF XY: 0.285 AC XY: 21203 AN XY: 74280

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.342

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.263

Gnomad4 SAS AF: 0.238

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.219

Gnomad4 OTH AF: 0.266

Alfa AF: 0.249 Hom.: 1615

Bravo AF: 0.292

Asia WGS AF: 0.305 AC: 1059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.2
DANN	Benign	0.51

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: rs10930939; hg19: chr2-152979933;