chr4-102344566-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS1
The NM_001135146.2(SLC39A8):c.97G>A(p.Val33Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00067 in 1,552,182 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. V33V) has been classified as Likely benign.
Frequency
Consequence
NM_001135146.2 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 |
---|---|---|---|---|---|---|---|
SLC39A8 | NM_001135146.2 | c.97G>A | p.Val33Met | missense_variant | 2/9 | ENST00000356736.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC39A8 | ENST00000356736.5 | c.97G>A | p.Val33Met | missense_variant | 2/9 | 1 | NM_001135146.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000453 AC: 69AN: 152164Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000642 AC: 97AN: 151170Hom.: 0 AF XY: 0.000690 AC XY: 56AN XY: 81190
GnomAD4 exome AF: 0.000694 AC: 971AN: 1399900Hom.: 1 Cov.: 30 AF XY: 0.000735 AC XY: 508AN XY: 690842
GnomAD4 genome AF: 0.000453 AC: 69AN: 152282Hom.: 1 Cov.: 32 AF XY: 0.000430 AC XY: 32AN XY: 74452
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Apr 02, 2023 | Identified in a patient with impaired glycosylation, global psychomotor delay, epilepsy, cerebellar atrophy, hypotonia, scoliosis, and low manganese concentrations who also harbored a SLC39A8 variant in cis and another SLC39A8 variant in trans (Park et al., 2015); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 32753748, 35636252, 29453449, 26637979) - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at