rs35741412
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001128225.3(SLC39A13):c.119G>A(p.Arg40Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0189 in 1,613,426 control chromosomes in the GnomAD database, including 370 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001128225.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0120 AC: 1826AN: 152186Hom.: 20 Cov.: 32
GnomAD3 exomes AF: 0.0132 AC: 3312AN: 250168Hom.: 41 AF XY: 0.0131 AC XY: 1773AN XY: 135560
GnomAD4 exome AF: 0.0196 AC: 28693AN: 1461122Hom.: 350 Cov.: 73 AF XY: 0.0192 AC XY: 13948AN XY: 726896
GnomAD4 genome AF: 0.0120 AC: 1824AN: 152304Hom.: 20 Cov.: 32 AF XY: 0.0109 AC XY: 809AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:3
SLC39A13: BP4, BS1, BS2 -
- -
This variant is associated with the following publications: (PMID: 26091878, 27211562, 26925801) -
not specified Benign:1
- -
Ehlers-Danlos syndrome Benign:1
- -
Ehlers-Danlos syndrome, spondylocheirodysplastic type Benign:1
- -
Connective tissue disorder Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at