4-42001684-A-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_006345.4(SLC30A9):c.178A>T(p.Thr60Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,456,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_006345.4 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 |
---|---|---|---|---|---|---|---|
SLC30A9 | NM_006345.4 | c.178A>T | p.Thr60Ser | missense_variant | 2/18 | ENST00000264451.12 | |
SLC30A9 | XM_047449525.1 | c.178A>T | p.Thr60Ser | missense_variant | 2/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC30A9 | ENST00000264451.12 | c.178A>T | p.Thr60Ser | missense_variant | 2/18 | 1 | NM_006345.4 | P1 | |
SLC30A9 | ENST00000510460.1 | n.303A>T | non_coding_transcript_exon_variant | 2/4 | 2 | ||||
SLC30A9 | ENST00000513699.5 | c.178A>T | p.Thr60Ser | missense_variant, NMD_transcript_variant | 2/19 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250434Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135484
GnomAD4 exome AF: 0.00000206 AC: 3AN: 1456586Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 725020
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.178A>T (p.T60S) alteration is located in exon 2 (coding exon 2) of the SLC30A9 gene. This alteration results from a A to T substitution at nucleotide position 178, causing the threonine (T) at amino acid position 60 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