chr8-22404768-G-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBS1_Supporting
The NM_015359.6(SLC39A14):c.58G>T(p.Gly20Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000867 in 1,613,874 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015359.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A14 | NM_001128431.4 | c.58G>T | p.Gly20Cys | missense_variant | 2/9 | ENST00000381237.6 | NP_001121903.1 | |
SLC39A14 | NM_015359.6 | c.58G>T | p.Gly20Cys | missense_variant | 2/9 | ENST00000359741.10 | NP_056174.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A14 | ENST00000359741.10 | c.58G>T | p.Gly20Cys | missense_variant | 2/9 | 2 | NM_015359.6 | ENSP00000352779 | A2 | |
SLC39A14 | ENST00000381237.6 | c.58G>T | p.Gly20Cys | missense_variant | 2/9 | 1 | NM_001128431.4 | ENSP00000370635 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152124Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251284Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461632Hom.: 1 Cov.: 35 AF XY: 0.0000151 AC XY: 11AN XY: 727146
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152242Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74434
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 03, 2021 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The cysteine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. This variant has not been reported in the literature in individuals affected with SLC39A14-related conditions. This variant is present in population databases (rs183988980, ExAC 0.01%). This sequence change replaces glycine with cysteine at codon 20 of the SLC39A14 protein (p.Gly20Cys). The glycine residue is weakly conserved and there is a large physicochemical difference between glycine and cysteine. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at