rs13266634
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PM2_SupportingBP4_StrongBP7
The NM_173851.3(SLC30A8):c.973C>A(p.Arg325=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000658 in 152056 control chromosomes in the gnomAD Genomes database, with no homozygous occurrence. 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 0.0000066 ( 0 hom., cov: 33)
Consequence
SLC30A8
NM_173851.3 synonymous
NM_173851.3 synonymous
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.742
Links
ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant; Number of alleles below threshold, gnomad allele frequency = 0.00000658 (1/152056) while in subpopulation AFR AF= 0.0000241 (1/41428). AF 95% confidence interval is 0. There are 0 homozygotes in gnomad. There are 1 alleles in male gnomad subpopulation. Median coverage is 33. This position pass quality control queck.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.5).
BP7
?
Synonymous conserved (PhyloP=-0.742 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.973C>A | p.Arg325= | synonymous_variant | 8/8 | ENST00000456015.7 | |
LOC105375716 | XR_007061067.1 | n.819+71G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.973C>A | p.Arg325= | synonymous_variant | 8/8 | 1 | NM_173851.3 | P1 | |
SLC30A8 | ENST00000519688.5 | c.826C>A | p.Arg276= | synonymous_variant | 9/9 | 1 | |||
SLC30A8 | ENST00000521243.5 | c.826C>A | p.Arg276= | synonymous_variant | 10/10 | 1 | |||
SLC30A8 | ENST00000427715.2 | c.826C>A | p.Arg276= | synonymous_variant | 11/11 | 2 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152056Hom.: 0 Cov.: 33
GnomAD3 genomes
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1
AN:
152056
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Cov.:
33
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
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