chr12-56231297-A-G
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_173596.3(SLC39A5):c.23A>G(p.His8Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000041 in 1,610,296 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173596.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A5 | NM_173596.3 | c.23A>G | p.His8Arg | missense_variant | 4/13 | ENST00000454355.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A5 | ENST00000454355.7 | c.23A>G | p.His8Arg | missense_variant | 4/13 | 1 | NM_173596.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000223 AC: 34AN: 152172Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000610 AC: 15AN: 245926Hom.: 0 AF XY: 0.0000300 AC XY: 4AN XY: 133492
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1458006Hom.: 0 Cov.: 34 AF XY: 0.0000110 AC XY: 8AN XY: 725018
GnomAD4 genome ? AF: 0.000223 AC: 34AN: 152290Hom.: 0 Cov.: 32 AF XY: 0.000228 AC XY: 17AN XY: 74460
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 07, 2023 | The c.23A>G (p.H8R) alteration is located in exon 4 (coding exon 1) of the SLC39A5 gene. This alteration results from a A to G substitution at nucleotide position 23, causing the histidine (H) at amino acid position 8 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