chr12-56232789-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_173596.3(SLC39A5):c.388C>T(p.Arg130Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0014 in 1,612,570 control chromosomes in the GnomAD database, including 38 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R130H) has been classified as Likely benign.
Frequency
Consequence
NM_173596.3 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 |
---|---|---|---|---|---|---|---|
SLC39A5 | NM_173596.3 | c.388C>T | p.Arg130Cys | missense_variant | 5/13 | ENST00000454355.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A5 | ENST00000454355.7 | c.388C>T | p.Arg130Cys | missense_variant | 5/13 | 1 | NM_173596.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00741 AC: 1127AN: 152162Hom.: 19 Cov.: 30
GnomAD3 exomes AF: 0.00196 AC: 488AN: 249112Hom.: 7 AF XY: 0.00144 AC XY: 194AN XY: 134876
GnomAD4 exome AF: 0.000777 AC: 1134AN: 1460290Hom.: 19 Cov.: 31 AF XY: 0.000626 AC XY: 455AN XY: 726574
GnomAD4 genome AF: 0.00741 AC: 1129AN: 152280Hom.: 19 Cov.: 30 AF XY: 0.00728 AC XY: 542AN XY: 74456
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 13, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at