chr10-117244034-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_003054.6(SLC18A2):c.185C>T(p.Thr62Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000867 in 1,614,038 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. T62T) has been classified as Likely benign.
Frequency
Consequence
NM_003054.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC18A2 | NM_003054.6 | c.185C>T | p.Thr62Met | missense_variant | 3/16 | ENST00000644641.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC18A2 | ENST00000644641.2 | c.185C>T | p.Thr62Met | missense_variant | 3/16 | NM_003054.6 | P1 | ||
SLC18A2 | ENST00000497497.1 | n.328C>T | non_coding_transcript_exon_variant | 3/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000125 AC: 19AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000179 AC: 45AN: 251304Hom.: 1 AF XY: 0.000162 AC XY: 22AN XY: 135856
GnomAD4 exome AF: 0.0000828 AC: 121AN: 1461868Hom.: 1 Cov.: 31 AF XY: 0.0000811 AC XY: 59AN XY: 727240
GnomAD4 genome ? AF: 0.000125 AC: 19AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74346
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at