rs3733047

Variant names:

• chr3-52837913-G-A
• rs3733047
• NM_198563.5:c.*2581C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-52837913-G-A
• chr3-52837913-G-C

Variant summary

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

The NM_198563.5(STIMATE):​c.*2581C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.246 in 152,110 control chromosomes in the GnomAD database, including 4,874 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 0.25 (4874 hom., cov: 33)
  • Exomes 𝑓: 0.19 (0 hom.)
• Consequence: STIMATE NM_198563.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11

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:38834): (STIMATE-MUSTN1 readthrough) This locus represents naturally occurring read-through transcription between the neighboring TMEM110 (transmembrane protein 110) and MUSTN1 (musculoskeletal, embryonic nuclear protein 1) genes. The read-through transcript encodes a fusion protein that shares sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STIMATE	NM_198563.5	c.*2581C>T		3_prime_UTR_variant	Exon 8 of 8	ENST00000355083.11	NP_940965.1
STIMATE-MUSTN1	NM_001198974.3	c.879+2587C>T		intron_variant	Intron 8 of 9		NP_001185903.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STIMATE	ENST00000355083	c.*2581C>T		3_prime_UTR_variant	Exon 8 of 8	1	NM_198563.5	ENSP00000347195.5
STIMATE-MUSTN1	ENST00000504329.1	c.879+2587C>T		intron_variant	Intron 8 of 9	5		ENSP00000422941.1

Frequencies

GnomAD3 genomes AF: 0.246 AC: 37378 AN: 151950 Hom.: 4872 Cov.: 33

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.403

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.320

Gnomad SAS AF: 0.128

Gnomad FIN AF: 0.258

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.243

GnomAD4 exome AF: 0.190 AC: 8 AN: 42 Hom.: 0 Cov.: 0 AF XY: 0.214 AC XY: 6 AN XY: 28

Gnomad4 AFR exome AF: 0.250

Gnomad4 SAS exome AF: 0.500

Gnomad4 FIN exome AF: 0.200

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.246 AC: 37409 AN: 152068 Hom.: 4874 Cov.: 33 AF XY: 0.248 AC XY: 18435 AN XY: 74332

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.320

Gnomad4 SAS AF: 0.128

Gnomad4 FIN AF: 0.258

Gnomad4 NFE AF: 0.234

Gnomad4 OTH AF: 0.246

Alfa AF: 0.203 Hom.: 700

Bravo AF: 0.257

Asia WGS AF: 0.236 AC: 820 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.8
DANN	Benign	0.41

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: rs3733047; hg19: chr3-52871929;