chr1-29121198-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001003682.4(TMEM200B):c.631G>A(p.Ala211Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,613,314 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001003682.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM200B | ENST00000521452.2 | c.631G>A | p.Ala211Thr | missense_variant | Exon 2 of 2 | 1 | NM_001003682.4 | ENSP00000428459.1 | ||
TMEM200B | ENST00000420504.2 | c.631G>A | p.Ala211Thr | missense_variant | Exon 2 of 2 | 1 | ENSP00000428544.1 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249792Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135546
GnomAD4 exome AF: 0.0000698 AC: 102AN: 1461138Hom.: 0 Cov.: 31 AF XY: 0.0000550 AC XY: 40AN XY: 726894
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152176Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.631G>A (p.A211T) alteration is located in exon 2 (coding exon 1) of the TMEM200B gene. This alteration results from a G to A substitution at nucleotide position 631, causing the alanine (A) at amino acid position 211 to be replaced by a threonine (T). 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