chr2-152124821-G-T

Position:

• chr2-152124821-G-T

Variant summary

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

The NM_005843.6(STAM2):​c.1180-886C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,148 control chromosomes in the GnomAD database, including 2,400 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 0.14 (2400 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: STAM2 NM_005843.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.559 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STAM2	NM_005843.6	c.1180-886C>A		intron_variant		ENST00000263904.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STAM2	ENST00000263904.5	c.1180-886C>A		intron_variant		1	NM_005843.6	P1

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21870 AN: 152028 Hom.: 2398 Cov.: 33

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0790

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.144 AC: 21897 AN: 152148 Hom.: 2400 Cov.: 33 AF XY: 0.150 AC XY: 11166 AN XY: 74368

Gnomad4 AFR AF: 0.199

Gnomad4 AMR AF: 0.0789

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.577

Gnomad4 SAS AF: 0.308

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.116

Alfa AF: 0.0890 Hom.: 1061

Bravo AF: 0.139

Asia WGS AF: 0.363 AC: 1262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.59

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: rs16830728; hg19: chr2-152981335;