chr2-27257318-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_003459.5(SLC30A3):c.613C>A(p.His205Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,612,918 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H205D) has been classified as Uncertain significance.
Frequency
Consequence
NM_003459.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A3 | NM_003459.5 | c.613C>A | p.His205Asn | missense_variant | 5/8 | ENST00000233535.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A3 | ENST00000233535.9 | c.613C>A | p.His205Asn | missense_variant | 5/8 | 1 | NM_003459.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152032Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000106 AC: 26AN: 244680Hom.: 0 AF XY: 0.000113 AC XY: 15AN XY: 133218
GnomAD4 exome AF: 0.0000678 AC: 99AN: 1460886Hom.: 0 Cov.: 31 AF XY: 0.0000702 AC XY: 51AN XY: 726708
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152032Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74244
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 06, 2021 | The c.613C>A (p.H205N) alteration is located in exon 5 (coding exon 5) of the SLC30A3 gene. This alteration results from a C to A substitution at nucleotide position 613, causing the histidine (H) at amino acid position 205 to be replaced by an asparagine (N). 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