16-48543154-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_153029.4(N4BP1):c.2441G>A(p.Arg814Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0058 in 1,603,822 control chromosomes in the GnomAD database, including 57 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_153029.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
N4BP1 | ENST00000262384.4 | c.2441G>A | p.Arg814Gln | missense_variant | Exon 7 of 7 | 1 | NM_153029.4 | ENSP00000262384.3 | ||
N4BP1 | ENST00000565423.5 | n.275G>A | non_coding_transcript_exon_variant | Exon 3 of 3 | 4 | |||||
N4BP1 | ENST00000569027.1 | n.*10G>A | downstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00624 AC: 950AN: 152186Hom.: 5 Cov.: 33
GnomAD3 exomes AF: 0.00715 AC: 1753AN: 245084Hom.: 17 AF XY: 0.00684 AC XY: 910AN XY: 133094
GnomAD4 exome AF: 0.00575 AC: 8346AN: 1451518Hom.: 52 Cov.: 31 AF XY: 0.00559 AC XY: 4026AN XY: 719868
GnomAD4 genome AF: 0.00624 AC: 951AN: 152304Hom.: 5 Cov.: 33 AF XY: 0.00736 AC XY: 548AN XY: 74474
ClinVar
Submissions by phenotype
not provided Benign:1
N4BP1: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at