chr4-42001758-A-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_006345.4(SLC30A9):c.252A>T(p.Glu84Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00042 in 1,609,732 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006345.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.252A>T | p.Glu84Asp | missense_variant | 2/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.252A>T | p.Glu84Asp | missense_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.252A>T | p.Glu84Asp | missense_variant | 2/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.377A>T | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.252A>T | p.Glu84Asp | missense_variant, NMD_transcript_variant | 2/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00211 AC: 321AN: 152058Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000534 AC: 132AN: 247122Hom.: 1 AF XY: 0.000404 AC XY: 54AN XY: 133744
GnomAD4 exome AF: 0.000244 AC: 356AN: 1457556Hom.: 2 Cov.: 31 AF XY: 0.000228 AC XY: 165AN XY: 725140
GnomAD4 genome ? AF: 0.00210 AC: 320AN: 152176Hom.: 0 Cov.: 32 AF XY: 0.00192 AC XY: 143AN XY: 74398
ClinVar
Submissions by phenotype
SLC30A9-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 24, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at