chr1-9601192-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_ModerateBP6_Moderate
The NM_001130924.3(TMEM201):c.694G>A(p.Ala232Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000062 in 1,612,788 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A232V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130924.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM201 | NM_001130924.3 | c.694G>A | p.Ala232Thr | missense_variant | 5/11 | ENST00000340381.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM201 | ENST00000340381.11 | c.694G>A | p.Ala232Thr | missense_variant | 5/11 | 5 | NM_001130924.3 | P1 | |
TMEM201 | ENST00000416541.5 | c.424G>A | p.Ala142Thr | missense_variant | 3/8 | 1 | |||
TMEM201 | ENST00000340305.9 | c.694G>A | p.Ala232Thr | missense_variant | 5/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000760 AC: 19AN: 250062Hom.: 0 AF XY: 0.0000739 AC XY: 10AN XY: 135294
GnomAD4 exome AF: 0.0000630 AC: 92AN: 1460570Hom.: 0 Cov.: 32 AF XY: 0.0000592 AC XY: 43AN XY: 726568
GnomAD4 genome AF: 0.0000526 AC: 8AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74360
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 26, 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