11-47415321-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP6_Very_StrongBS2
The NM_001128225.3(SLC39A13):c.1074G>A(p.Ala358=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000295 in 1,614,040 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Synonymous variant affecting the same amino acid position (i.e. A358A) has been classified as Likely benign.
Frequency
Consequence
NM_001128225.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC39A13 | NM_001128225.3 | c.1074G>A | p.Ala358= | synonymous_variant | 10/10 | ENST00000362021.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A13 | ENST00000362021.9 | c.1074G>A | p.Ala358= | synonymous_variant | 10/10 | 1 | NM_001128225.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152136Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000660 AC: 166AN: 251362Hom.: 1 AF XY: 0.000898 AC XY: 122AN XY: 135872
GnomAD4 exome AF: 0.000312 AC: 456AN: 1461786Hom.: 3 Cov.: 35 AF XY: 0.000451 AC XY: 328AN XY: 727204
GnomAD4 genome AF: 0.000131 AC: 20AN: 152254Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74442
ClinVar
Submissions by phenotype
SLC39A13-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 23, 2022 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Ehlers-Danlos syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 07, 2022 | - - |
Ehlers-Danlos syndrome, spondylocheirodysplastic type Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 17, 2024 | - - |
Connective tissue disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 07, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at