rs2234632
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The ENST00000298681.5(SLC39A2):c.128T>A(p.Leu43Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,613,950 control chromosomes in the GnomAD database, including 40 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L43R) has been classified as Benign.
Frequency
Consequence
ENST00000298681.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC39A2 | NM_014579.4 | c.128T>A | p.Leu43Gln | missense_variant | 2/4 | ENST00000298681.5 | NP_055394.2 | |
SLC39A2 | NM_001256588.2 | c.128T>A | p.Leu43Gln | missense_variant | 2/4 | NP_001243517.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC39A2 | ENST00000298681.5 | c.128T>A | p.Leu43Gln | missense_variant | 2/4 | 1 | NM_014579.4 | ENSP00000298681 | P1 | |
SLC39A2 | ENST00000554422.5 | c.128T>A | p.Leu43Gln | missense_variant | 2/4 | 1 | ENSP00000452568 | |||
ENST00000647921.1 | n.474A>T | non_coding_transcript_exon_variant | 2/5 | |||||||
SLC39A2 | ENST00000554128.1 | n.284T>A | non_coding_transcript_exon_variant | 2/2 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00848 AC: 1289AN: 152008Hom.: 19 Cov.: 31
GnomAD3 exomes AF: 0.00210 AC: 527AN: 251294Hom.: 8 AF XY: 0.00151 AC XY: 205AN XY: 135854
GnomAD4 exome AF: 0.000881 AC: 1288AN: 1461826Hom.: 21 Cov.: 48 AF XY: 0.000762 AC XY: 554AN XY: 727220
GnomAD4 genome AF: 0.00847 AC: 1289AN: 152124Hom.: 19 Cov.: 31 AF XY: 0.00796 AC XY: 592AN XY: 74346
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at