chr19-55320439-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001282011.2(TMEM150B):āc.148C>Gā(p.Pro50Ala) variant causes a missense change. The variant allele was found at a frequency of 0.0000774 in 1,589,056 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P50S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001282011.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMEM150B | NM_001282011.2 | c.148C>G | p.Pro50Ala | missense_variant | 5/8 | ENST00000326652.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMEM150B | ENST00000326652.9 | c.148C>G | p.Pro50Ala | missense_variant | 5/8 | 1 | NM_001282011.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000920 AC: 14AN: 152110Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000109 AC: 25AN: 229872Hom.: 0 AF XY: 0.0000886 AC XY: 11AN XY: 124098
GnomAD4 exome AF: 0.0000759 AC: 109AN: 1436828Hom.: 0 Cov.: 33 AF XY: 0.0000730 AC XY: 52AN XY: 711958
GnomAD4 genome AF: 0.0000920 AC: 14AN: 152228Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74430
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.148C>G (p.P50A) alteration is located in exon 5 (coding exon 3) of the TMEM150B gene. This alteration results from a C to G substitution at nucleotide position 148, causing the proline (P) at amino acid position 50 to be replaced by an alanine (A). 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