rs10263
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_020860.4(STIM2):c.*879A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,668 control chromosomes in the GnomAD database, including 971 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 0.10 ( 971 hom., cov: 32)
Exomes 𝑓: 0.071 ( 0 hom. )
Consequence
STIM2
NM_020860.4 3_prime_UTR
NM_020860.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.719
Genes affected
STIM2 (HGNC:19205): (stromal interaction molecule 2) This gene is a member of the stromal interaction molecule (STIM) family and likely arose, along with related family member STIM1, from a common ancestral gene. The encoded protein functions to regulate calcium concentrations in the cytosol and endoplasmic reticulum, and is involved in the activation of plasma membrane Orai Ca(2+) entry channels. This gene initiates translation from a non-AUG (UUG) start site. A signal peptide is cleaved from the resulting protein. Multiple transcript variants result from alternative splicing. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.49).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.318 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
STIM2 | NM_020860.4 | c.*879A>G | 3_prime_UTR_variant | Exon 12 of 12 | ENST00000467087.7 | NP_065911.3 | ||
STIM2 | NM_001169118.2 | c.*879A>G | 3_prime_UTR_variant | Exon 13 of 13 | NP_001162589.1 | |||
STIM2 | NM_001169117.2 | c.*1388A>G | 3_prime_UTR_variant | Exon 13 of 13 | NP_001162588.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
STIM2 | ENST00000467087.7 | c.*879A>G | 3_prime_UTR_variant | Exon 12 of 12 | 1 | NM_020860.4 | ENSP00000419073.2 |
Frequencies
GnomAD3 genomes AF: 0.102 AC: 15467AN: 152112Hom.: 975 Cov.: 32
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GnomAD4 exome AF: 0.0708 AC: 31AN: 438Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 19AN XY: 266
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GnomAD4 genome AF: 0.102 AC: 15460AN: 152230Hom.: 971 Cov.: 32 AF XY: 0.106 AC XY: 7873AN XY: 74440
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ClinVar
Not reported inComputational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at