chr19-55320979-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001282011.2(TMEM150B):c.58G>T(p.Val20Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,768 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 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. V20I) has been classified as Likely benign.
Frequency
Consequence
NM_001282011.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM150B | NM_001282011.2 | c.58G>T | p.Val20Phe | missense_variant | 3/8 | ENST00000326652.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM150B | ENST00000326652.9 | c.58G>T | p.Val20Phe | missense_variant | 3/8 | 1 | NM_001282011.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000803 AC: 2AN: 248994Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135090
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461614Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 727122
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74326
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.58G>T (p.V20F) alteration is located in exon 3 (coding exon 1) of the TMEM150B gene. This alteration results from a G to T substitution at nucleotide position 58, causing the valine (V) at amino acid position 20 to be replaced by a phenylalanine (F). 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