rs200185429
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP6
The NM_173851.3(SLC30A8):c.412C>T(p.Arg138Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000139 in 1,606,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as protective (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_173851.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A8 | NM_173851.3 | c.412C>T | p.Arg138Ter | stop_gained | 3/8 | ENST00000456015.7 | |
LOC105375716 | XR_007061067.1 | n.819+19531G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A8 | ENST00000456015.7 | c.412C>T | p.Arg138Ter | stop_gained | 3/8 | 1 | NM_173851.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000105 AC: 16AN: 152054Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000238 AC: 59AN: 247592Hom.: 0 AF XY: 0.000299 AC XY: 40AN XY: 133764
GnomAD4 exome AF: 0.000143 AC: 208AN: 1453950Hom.: 0 Cov.: 31 AF XY: 0.000167 AC XY: 121AN XY: 723016
GnomAD4 genome ? AF: 0.000105 AC: 16AN: 152172Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74398
ClinVar
Submissions by phenotype
Type 2 diabetes mellitus Benign:1
protective, no assertion criteria provided | literature only | OMIM | Apr 01, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at