chr1-9598512-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001130924.3(TMEM201):c.493C>T(p.Arg165Trp) variant causes a missense change. The variant allele was found at a frequency of 0.00000991 in 1,613,876 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R165Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001130924.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM201 | NM_001130924.3 | c.493C>T | p.Arg165Trp | missense_variant | 4/11 | ENST00000340381.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM201 | ENST00000340381.11 | c.493C>T | p.Arg165Trp | missense_variant | 4/11 | 5 | NM_001130924.3 | P1 | |
TMEM201 | ENST00000416541.5 | c.223C>T | p.Arg75Trp | missense_variant | 2/8 | 1 | |||
TMEM201 | ENST00000340305.9 | c.493C>T | p.Arg165Trp | missense_variant | 4/6 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250964Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135828
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461652Hom.: 0 Cov.: 48 AF XY: 0.0000110 AC XY: 8AN XY: 727126
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152224Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | The c.493C>T (p.R165W) alteration is located in exon 4 (coding exon 4) of the TMEM201 gene. This alteration results from a C to T substitution at nucleotide position 493, causing the arginine (R) at amino acid position 165 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at