1-29121548-A-C
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_001003682.4(TMEM200B):c.281T>G(p.Met94Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00226 in 1,508,372 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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 Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TMEM200B | ENST00000521452.2 | c.281T>G | p.Met94Arg | missense_variant | Exon 2 of 2 | 1 | NM_001003682.4 | ENSP00000428459.1 | ||
TMEM200B | ENST00000420504.2 | c.281T>G | p.Met94Arg | missense_variant | Exon 2 of 2 | 1 | ENSP00000428544.1 |
Frequencies
GnomAD3 genomes AF: 0.00142 AC: 216AN: 151656Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00114 AC: 118AN: 103874Hom.: 0 AF XY: 0.00104 AC XY: 61AN XY: 58510
GnomAD4 exome AF: 0.00236 AC: 3201AN: 1356608Hom.: 5 Cov.: 31 AF XY: 0.00227 AC XY: 1520AN XY: 669808
GnomAD4 genome AF: 0.00142 AC: 215AN: 151764Hom.: 0 Cov.: 32 AF XY: 0.00132 AC XY: 98AN XY: 74192
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.281T>G (p.M94R) alteration is located in exon 2 (coding exon 1) of the TMEM200B gene. This alteration results from a T to G substitution at nucleotide position 281, causing the methionine (M) at amino acid position 94 to be replaced by an arginine (R). 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