chr20-5069280-T-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The ENST00000612323.4(TMEM230):c.292A>C(p.Met98Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000424 in 1,536,024 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
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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 |
---|---|---|---|---|---|---|---|
TMEM230 | NM_001330987.2 | c.292A>C | p.Met98Leu | missense_variant | 4/4 | ||
TMEM230 | XR_002958476.2 | n.529A>C | non_coding_transcript_exon_variant | 5/7 | |||
TMEM230 | XR_002958478.2 | n.423A>C | non_coding_transcript_exon_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM230 | ENST00000612323.4 | c.292A>C | p.Met98Leu | missense_variant | 4/4 | 1 | |||
TMEM230 | ENST00000615008.4 | c.292A>C | p.Met98Leu | missense_variant | 5/6 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.00200 AC: 304AN: 152166Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000379 AC: 51AN: 134408Hom.: 0 AF XY: 0.000383 AC XY: 28AN XY: 73196
GnomAD4 exome AF: 0.000249 AC: 344AN: 1383740Hom.: 1 Cov.: 31 AF XY: 0.000221 AC XY: 151AN XY: 682808
GnomAD4 genome ? AF: 0.00202 AC: 307AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.00179 AC XY: 133AN XY: 74460
ClinVar
Submissions by phenotype
TMEM230-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 11, 2021 | 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