chr2-672826-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_152834.4(TMEM18):c.215C>T(p.Ala72Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000503 in 1,479,316 control chromosomes in the GnomAD database, including 3 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_152834.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TMEM18 | NM_152834.4 | c.215C>T | p.Ala72Val | missense_variant | 3/5 | ENST00000281017.8 | NP_690047.2 | |
TMEM18 | NM_001352681.1 | c.224C>T | p.Ala75Val | missense_variant | 3/5 | NP_001339610.1 | ||
TMEM18 | NM_001352680.2 | c.176C>T | p.Ala59Val | missense_variant | 4/6 | NP_001339609.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM18 | ENST00000281017.8 | c.215C>T | p.Ala72Val | missense_variant | 3/5 | 1 | NM_152834.4 | ENSP00000281017 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000526 AC: 80AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000623 AC: 99AN: 158986Hom.: 1 AF XY: 0.000543 AC XY: 48AN XY: 88420
GnomAD4 exome AF: 0.000500 AC: 664AN: 1327000Hom.: 3 Cov.: 31 AF XY: 0.000529 AC XY: 345AN XY: 651850
GnomAD4 genome AF: 0.000525 AC: 80AN: 152316Hom.: 0 Cov.: 33 AF XY: 0.000403 AC XY: 30AN XY: 74476
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 07, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at