rs583362
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_003063.3(SLN):c.-65G>C variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.58 in 1,067,646 control chromosomes in the GnomAD database, including 180,634 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 0.60 ( 28174 hom., cov: 31)
Exomes 𝑓: 0.58 ( 152460 hom. )
Consequence
SLN
NM_003063.3 5_prime_UTR
NM_003063.3 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.843
Genes affected
SLN (HGNC:11089): (sarcolipin) Sarcoplasmic reticulum Ca(2+)-ATPases are transmembrane proteins that catalyze the ATP-dependent transport of Ca(2+) from the cytosol into the lumen of the sarcoplasmic reticulum in muscle cells. This gene encodes a small proteolipid that regulates several sarcoplasmic reticulum Ca(2+)-ATPases. The transmembrane protein interacts with Ca(2+)-ATPases and reduces the accumulation of Ca(2+) in the sarcoplasmic reticulum without affecting the rate of ATP hydrolysis. [provided by RefSeq, Jul 2008]
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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=-0.76).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLN | NM_003063.3 | c.-65G>C | 5_prime_UTR_variant | 2/2 | ENST00000305991.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLN | ENST00000305991.3 | c.-65G>C | 5_prime_UTR_variant | 2/2 | 1 | NM_003063.3 | P1 | ||
SLN | ENST00000525934.1 | c.-65G>C | 5_prime_UTR_variant | 2/2 | 3 | P1 | |||
SLN | ENST00000531293.1 | c.-65G>C | 5_prime_UTR_variant | 3/3 | 4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.603 AC: 91548AN: 151832Hom.: 28136 Cov.: 31
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GnomAD4 exome AF: 0.576 AC: 527292AN: 915696Hom.: 152460 Cov.: 12 AF XY: 0.570 AC XY: 272891AN XY: 479016
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GnomAD4 genome ? AF: 0.603 AC: 91641AN: 151950Hom.: 28174 Cov.: 31 AF XY: 0.610 AC XY: 45269AN XY: 74252
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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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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at