rs10497095

chr2-152121474-G-A

Variant summary

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

The NM_005843.6(STAM2):c.1350-672C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 152,000 control chromosomes in the GnomAD database, including 3,617 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 0.21 (3617 hom., cov: 31)
• Consequence: STAM2 NM_005843.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23

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=-0.85).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAM2	NM_005843.6	c.1350-672C>T		intron_variant		ENST00000263904.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAM2	ENST00000263904.5	c.1350-672C>T		intron_variant		1	NM_005843.6	P1
STAM2	ENST00000489389.1	n.922-672C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.211 AC: 32094 AN: 151884 Hom.: 3600 Cov.: 31

Gnomad AFR AF: 0.153

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.193

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

GnomAD4 genome AF: 0.212 AC: 32154 AN: 152000 Hom.: 3617 Cov.: 31 AF XY: 0.216 AC XY: 16079 AN XY: 74278

Gnomad4 AFR AF: 0.153

Gnomad4 AMR AF: 0.301

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.208

Gnomad4 OTH AF: 0.203

Alfa AF: 0.194 Hom.: 437

Bravo AF: 0.212

Asia WGS AF: 0.280 AC: 973 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	1.2
Dann	Benign	0.68

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: rs10497095; hg19: chr2-152977988;