2-27255359-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003459.5(SLC30A3):c.1120C>T(p.Pro374Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000147 in 1,614,208 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003459.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC30A3 | NM_003459.5 | c.1120C>T | p.Pro374Ser | missense_variant | 8/8 | ENST00000233535.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A3 | ENST00000233535.9 | c.1120C>T | p.Pro374Ser | missense_variant | 8/8 | 1 | NM_003459.5 | P1 | |
SLC30A3 | ENST00000482990.1 | n.1935C>T | non_coding_transcript_exon_variant | 3/3 | 2 | ||||
SLC30A3 | ENST00000497341.5 | n.1773C>T | non_coding_transcript_exon_variant | 4/4 | 2 | ||||
SLC30A3 | ENST00000445870.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152226Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000223 AC: 56AN: 251014Hom.: 0 AF XY: 0.000339 AC XY: 46AN XY: 135800
GnomAD4 exome AF: 0.000152 AC: 222AN: 1461864Hom.: 0 Cov.: 31 AF XY: 0.000180 AC XY: 131AN XY: 727232
GnomAD4 genome AF: 0.000105 AC: 16AN: 152344Hom.: 0 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74500
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 26, 2024 | The c.1120C>T (p.P374S) alteration is located in exon 8 (coding exon 8) of the SLC30A3 gene. This alteration results from a C to T substitution at nucleotide position 1120, causing the proline (P) at amino acid position 374 to be replaced by a serine (S). 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