chr9-16419500-T-C
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_017637.6(BNC2):c.2789A>G(p.Asp930Gly) variant causes a missense change. The variant allele was found at a frequency of 0.0033 in 1,614,038 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D930N) has been classified as Likely benign.
Frequency
Consequence
NM_017637.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNC2 | NM_017637.6 | c.2789A>G | p.Asp930Gly | missense_variant | 7/7 | ENST00000380672.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNC2 | ENST00000380672.9 | c.2789A>G | p.Asp930Gly | missense_variant | 7/7 | 2 | NM_017637.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.00260 AC: 395AN: 152044Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00267 AC: 671AN: 250904Hom.: 3 AF XY: 0.00250 AC XY: 339AN XY: 135640
GnomAD4 exome AF: 0.00338 AC: 4938AN: 1461874Hom.: 12 Cov.: 35 AF XY: 0.00328 AC XY: 2382AN XY: 727238
GnomAD4 genome ? AF: 0.00260 AC: 395AN: 152164Hom.: 0 Cov.: 31 AF XY: 0.00241 AC XY: 179AN XY: 74396
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | BNC2: BP4, BS2 - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 30, 2023 | - - |
BNC2-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Aug 10, 2021 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Hypotension Other:1
not provided, no classification provided | literature only | Centre for molecular medicine, Karolinska Institutet | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at