20-5069330-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000612323.4(TMEM230):c.242G>A(p.Arg81Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000321 in 1,534,844 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 6/7 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
ENST00000612323.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM230 | NM_001330987.2 | c.242G>A | p.Arg81Gln | missense_variant | 4/4 | ||
TMEM230 | XR_002958476.2 | n.479G>A | non_coding_transcript_exon_variant | 5/7 | |||
TMEM230 | XR_002958478.2 | n.373G>A | non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM230 | ENST00000612323.4 | c.242G>A | p.Arg81Gln | missense_variant | 4/4 | 1 | |||
TMEM230 | ENST00000615008.4 | c.242G>A | p.Arg81Gln | missense_variant | 5/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00178 AC: 271AN: 152114Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000376 AC: 50AN: 132892Hom.: 0 AF XY: 0.000166 AC XY: 12AN XY: 72362
GnomAD4 exome AF: 0.000160 AC: 221AN: 1382612Hom.: 1 Cov.: 31 AF XY: 0.000116 AC XY: 79AN XY: 682246
GnomAD4 genome ? AF: 0.00179 AC: 272AN: 152232Hom.: 0 Cov.: 32 AF XY: 0.00179 AC XY: 133AN XY: 74434
ClinVar
Submissions by phenotype
TMEM230-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Nov 03, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at