chr16-4207312-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001098814.2(SRL):c.62-2678G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0307 in 456,846 control chromosomes in the GnomAD database, including 374 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 0.025 ( 95 hom., cov: 33)
Exomes 𝑓: 0.033 ( 279 hom. )
Consequence
SRL
NM_001098814.2 intron
NM_001098814.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.986
Genes affected
SRL (HGNC:11295): (sarcalumenin) Predicted to enable GTP binding activity. Predicted to be involved in endocytosis and endosomal transport. Predicted to act upstream of or within response to muscle activity involved in regulation of muscle adaptation and store-operated calcium entry. Predicted to be located in sarcoplasmic reticulum lumen and sarcoplasmic reticulum membrane. Predicted to be active in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.83).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0612 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SRL | NM_001098814.2 | c.62-2678G>A | intron_variant | ENST00000399609.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SRL | ENST00000399609.7 | c.62-2678G>A | intron_variant | 1 | NM_001098814.2 | P1 | |||
SRL | ENST00000572111.1 | c.854G>A | p.Ser285Asn | missense_variant, NMD_transcript_variant | 2/7 | 1 | |||
SRL | ENST00000537996.1 | c.-65-2678G>A | intron_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.0252 AC: 3842AN: 152204Hom.: 92 Cov.: 33
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GnomAD3 exomes AF: 0.0388 AC: 5328AN: 137192Hom.: 181 AF XY: 0.0358 AC XY: 2668AN XY: 74560
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GnomAD4 exome AF: 0.0334 AC: 10170AN: 304524Hom.: 279 Cov.: 0 AF XY: 0.0321 AC XY: 5560AN XY: 173392
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GnomAD4 genome AF: 0.0253 AC: 3849AN: 152322Hom.: 95 Cov.: 33 AF XY: 0.0257 AC XY: 1916AN XY: 74478
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ClinVar
Not reported inComputational scores
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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