chr4-42018125-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006345.4(SLC30A9):c.289A>G(p.Thr97Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.976 in 1,554,576 control chromosomes in the GnomAD database, including 740,322 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_006345.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.289A>G | p.Thr97Ala | missense_variant | 3/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.289A>G | p.Thr97Ala | missense_variant | 3/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.289A>G | p.Thr97Ala | missense_variant | 3/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.414A>G | non_coding_transcript_exon_variant | 3/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.289A>G | p.Thr97Ala | missense_variant, NMD_transcript_variant | 3/19 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.977 AC: 148500AN: 152060Hom.: 72529 Cov.: 31
GnomAD3 exomes AF: 0.980 AC: 242926AN: 247992Hom.: 118982 AF XY: 0.980 AC XY: 131456AN XY: 134200
GnomAD4 exome AF: 0.976 AC: 1368424AN: 1402398Hom.: 667732 Cov.: 23 AF XY: 0.976 AC XY: 683882AN XY: 700832
GnomAD4 genome ? AF: 0.977 AC: 148620AN: 152178Hom.: 72590 Cov.: 31 AF XY: 0.977 AC XY: 72665AN XY: 74392
ClinVar
Submissions by phenotype
Psychomotor regression-oculomotor apraxia-movement disorder-nephropathy syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Jul 15, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at