X-153504722-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001711.6(BGN):c.91G>T(p.Asp31Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.000000911 in 1,097,887 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. 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. D31N) has been classified as Uncertain significance.
Frequency
Consequence
NM_001711.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BGN | NM_001711.6 | c.91G>T | p.Asp31Tyr | missense_variant | 2/8 | ENST00000331595.9 | |
BGN | XM_017029724.3 | c.91G>T | p.Asp31Tyr | missense_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BGN | ENST00000331595.9 | c.91G>T | p.Asp31Tyr | missense_variant | 2/8 | 1 | NM_001711.6 | P1 | |
BGN | ENST00000431891.1 | c.91G>T | p.Asp31Tyr | missense_variant | 2/5 | 5 | |||
BGN | ENST00000472615.5 | n.235G>T | non_coding_transcript_exon_variant | 2/8 | 5 | ||||
BGN | ENST00000480756.1 | n.233G>T | non_coding_transcript_exon_variant | 2/8 | 5 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome AF: 9.11e-7 AC: 1AN: 1097887Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 363333
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 23, 2024 | This sequence change replaces aspartic acid, which is acidic and polar, with tyrosine, which is neutral and polar, at codon 31 of the BGN protein (p.Asp31Tyr). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with BGN-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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