rs3796352

chr3-52879263-C-T

Variant summary

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

The NM_198563.5(STIMATE):c.160+18028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0664 in 152,268 control chromosomes in the GnomAD database, including 421 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 0.066 (421 hom., cov: 32)
• Consequence: STIMATE NM_198563.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0340

Genes affected

STIMATE (HGNC:30526): (STIM activating enhancer) Enables calcium channel regulator activity. Involved in activation of store-operated calcium channel activity; calcium-mediated signaling using intracellular calcium source; and positive regulation of calcineurin-NFAT signaling cascade. Located in cortical endoplasmic reticulum; endoplasmic reticulum membrane; and endoplasmic reticulum-plasma membrane contact site. [provided by Alliance of Genome Resources, Apr 2022]

STIMATE-MUSTN1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0919 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STIMATE	NM_198563.5	c.160+18028G>A		intron_variant		ENST00000355083.11
STIMATE-MUSTN1	NM_001198974.3	c.160+18028G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STIMATE	ENST00000355083.11	c.160+18028G>A		intron_variant		1	NM_198563.5	P1
STIMATE	ENST00000467979.1	c.*40+16615G>A		intron_variant, NMD_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.0665 AC: 10112 AN: 152150 Hom.: 421 Cov.: 32

Gnomad AFR AF: 0.0181

Gnomad AMI AF: 0.0870

Gnomad AMR AF: 0.0918

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.0386

Gnomad SAS AF: 0.0392

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0832

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

GnomAD4 genome AF: 0.0664 AC: 10109 AN: 152268 Hom.: 421 Cov.: 32 AF XY: 0.0633 AC XY: 4715 AN XY: 74458

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0916

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.0387

Gnomad4 SAS AF: 0.0394

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.0828

Alfa AF: 0.0901 Hom.: 768

Bravo AF: 0.0680

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	4.5
Dann	Benign	0.45

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: rs3796352; hg19: chr3-52913279;