15-83258053-G-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_001717.4(BNC1):c.2374C>T(p.Arg792Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000744 in 1,613,558 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BNC1 | NM_001717.4 | c.2374C>T | p.Arg792Cys | missense_variant | 5/5 | ENST00000345382.7 | NP_001708.3 | |
BNC1 | NM_001301206.2 | c.2353C>T | p.Arg785Cys | missense_variant | 5/5 | NP_001288135.1 | ||
BNC1 | XM_011521893.2 | c.2299C>T | p.Arg767Cys | missense_variant | 5/5 | XP_011520195.1 | ||
BNC1 | XM_011521894.1 | c.2020C>T | p.Arg674Cys | missense_variant | 4/4 | XP_011520196.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BNC1 | ENST00000345382.7 | c.2374C>T | p.Arg792Cys | missense_variant | 5/5 | 1 | NM_001717.4 | ENSP00000307041.2 | ||
BNC1 | ENST00000569704.2 | c.2353C>T | p.Arg785Cys | missense_variant | 5/5 | 5 | ENSP00000456727.1 | |||
ENSG00000259986 | ENST00000565495.1 | n.264+72985G>A | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000788 AC: 12AN: 152218Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251290Hom.: 0 AF XY: 0.0000884 AC XY: 12AN XY: 135820
GnomAD4 exome AF: 0.0000739 AC: 108AN: 1461340Hom.: 0 Cov.: 31 AF XY: 0.0000674 AC XY: 49AN XY: 726844
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152218Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5AN XY: 74360
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2023 | The c.2374C>T (p.R792C) alteration is located in exon 5 (coding exon 5) of the BNC1 gene. This alteration results from a C to T substitution at nucleotide position 2374, causing the arginine (R) at amino acid position 792 to be replaced by a cysteine (C). 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