chr1-29121560-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.269G>A(p.Ser90Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000012 in 1,503,812 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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.269G>A | p.Ser90Asn | missense_variant | Exon 2 of 2 | 1 | NM_001003682.4 | ENSP00000428459.1 | ||
TMEM200B | ENST00000420504.2 | c.269G>A | p.Ser90Asn | missense_variant | Exon 2 of 2 | 1 | ENSP00000428544.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 151802Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000206 AC: 2AN: 97190Hom.: 0 AF XY: 0.0000363 AC XY: 2AN XY: 55154
GnomAD4 exome AF: 0.0000118 AC: 16AN: 1352010Hom.: 1 Cov.: 31 AF XY: 0.0000165 AC XY: 11AN XY: 667548
GnomAD4 genome AF: 0.0000132 AC: 2AN: 151802Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74152
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.269G>A (p.S90N) 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 269, causing the serine (S) at amino acid position 90 to be replaced by an asparagine (N). 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