chr19-41354720-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM1PM2
The NM_030578.4(B9D2):c.508C>T(p.Arg170Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000551 in 1,613,892 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. R170G) has been classified as Uncertain significance.
Frequency
Consequence
NM_030578.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B9D2 | NM_030578.4 | c.508C>T | p.Arg170Cys | missense_variant | 4/4 | ENST00000243578.8 | |
B9D2 | XM_011527349.3 | c.508C>T | p.Arg170Cys | missense_variant | 4/4 | ||
B9D2 | XM_011527350.3 | c.349C>T | p.Arg117Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B9D2 | ENST00000243578.8 | c.508C>T | p.Arg170Cys | missense_variant | 4/4 | 1 | NM_030578.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33
GnomAD4 exome AF: 0.0000595 AC: 87AN: 1461714Hom.: 0 Cov.: 32 AF XY: 0.0000440 AC XY: 32AN XY: 727160
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152178Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
Meckel-Gruber syndrome;C0431399:Familial aplasia of the vermis Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 19, 2022 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 170 of the B9D2 protein (p.Arg170Cys). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with B9D2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at