chr9-16419501-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_017637.6(BNC2):c.2788G>A(p.Asp930Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,614,122 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 Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D930G) 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BNC2 | NM_017637.6 | c.2788G>A | p.Asp930Asn | missense_variant | 7/7 | ENST00000380672.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BNC2 | ENST00000380672.9 | c.2788G>A | p.Asp930Asn | missense_variant | 7/7 | 2 | NM_017637.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152132Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000757 AC: 19AN: 250868Hom.: 0 AF XY: 0.0000664 AC XY: 9AN XY: 135630
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461872Hom.: 0 Cov.: 35 AF XY: 0.0000481 AC XY: 35AN XY: 727238
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152250Hom.: 0 Cov.: 31 AF XY: 0.000255 AC XY: 19AN XY: 74432
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.2788G>A (p.D930N) alteration is located in exon 7 (coding exon 7) of the BNC2 gene. This alteration results from a G to A substitution at nucleotide position 2788, causing the aspartic acid (D) at amino acid position 930 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 11, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at