1-153960280-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001271958.2(SLC39A1):c.793G>A(p.Gly265Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000843 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001271958.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A1 | ENST00000356205.9 | c.793G>A | p.Gly265Arg | missense_variant | Exon 4 of 4 | 1 | NM_001271958.2 | ENSP00000348535.4 | ||
ENSG00000285779 | ENST00000648921.1 | n.*881G>A | non_coding_transcript_exon_variant | Exon 6 of 6 | ENSP00000498105.1 | |||||
ENSG00000285779 | ENST00000648921.1 | n.*881G>A | 3_prime_UTR_variant | Exon 6 of 6 | ENSP00000498105.1 |
Frequencies
GnomAD3 genomes AF: 0.000151 AC: 23AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000144 AC: 36AN: 250800Hom.: 0 AF XY: 0.000125 AC XY: 17AN XY: 135738
GnomAD4 exome AF: 0.0000773 AC: 113AN: 1461732Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 727172
GnomAD4 genome AF: 0.000151 AC: 23AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000175 AC XY: 13AN XY: 74386
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.793G>A (p.G265R) alteration is located in exon 5 (coding exon 3) of the SLC39A1 gene. This alteration results from a G to A substitution at nucleotide position 793, causing the glycine (G) at amino acid position 265 to be replaced by an arginine (R). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at