chr19-41354712-G-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 2P and 11B. PM2BP4_StrongBP6_ModerateBP7BS1
The NM_030578.4(B9D2):c.516C>A(p.Gly172=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000547 in 1,461,704 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. G172G) has been classified as Likely benign.
Frequency
Consequence
NM_030578.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
B9D2 | NM_030578.4 | c.516C>A | p.Gly172= | synonymous_variant | 4/4 | ENST00000243578.8 | |
B9D2 | XM_011527349.3 | c.516C>A | p.Gly172= | synonymous_variant | 4/4 | ||
B9D2 | XM_011527350.3 | c.357C>A | p.Gly119= | synonymous_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
B9D2 | ENST00000243578.8 | c.516C>A | p.Gly172= | synonymous_variant | 4/4 | 1 | NM_030578.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.0000359 AC: 9AN: 250602Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135636
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461704Hom.: 0 Cov.: 32 AF XY: 0.00000688 AC XY: 5AN XY: 727166
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
B9D2-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 21, 2019 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at