15-83257950-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001717.4(BNC1):c.2477G>A(p.Arg826Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000595 in 1,614,018 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 Uncertain significance (★).
Frequency
Consequence
NM_001717.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BNC1 | NM_001717.4 | c.2477G>A | p.Arg826Gln | missense_variant | Exon 5 of 5 | ENST00000345382.7 | NP_001708.3 | |
BNC1 | NM_001301206.2 | c.2456G>A | p.Arg819Gln | missense_variant | Exon 5 of 5 | NP_001288135.1 | ||
BNC1 | XM_011521893.2 | c.2402G>A | p.Arg801Gln | missense_variant | Exon 5 of 5 | XP_011520195.1 | ||
BNC1 | XM_011521894.1 | c.2123G>A | p.Arg708Gln | missense_variant | Exon 4 of 4 | XP_011520196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BNC1 | ENST00000345382.7 | c.2477G>A | p.Arg826Gln | missense_variant | Exon 5 of 5 | 1 | NM_001717.4 | ENSP00000307041.2 | ||
BNC1 | ENST00000569704.2 | c.2456G>A | p.Arg819Gln | missense_variant | Exon 5 of 5 | 5 | ENSP00000456727.1 | |||
ENSG00000259986 | ENST00000565495.1 | n.264+72882C>T | intron_variant | Intron 1 of 1 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152200Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000796 AC: 20AN: 251366Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135852
GnomAD4 exome AF: 0.0000575 AC: 84AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.0000536 AC XY: 39AN XY: 727192
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152200Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2477G>A (p.R826Q) alteration is located in exon 5 (coding exon 5) of the BNC1 gene. This alteration results from a G to A substitution at nucleotide position 2477, causing the arginine (R) at amino acid position 826 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at