1-11858322-C-A
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002521.3(NPPB):c.280G>T(p.Val94Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00289 in 1,613,860 control chromosomes in the GnomAD database, including 15 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_002521.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00321 AC: 489AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.00335 AC: 839AN: 250716Hom.: 6 AF XY: 0.00356 AC XY: 482AN XY: 135500
GnomAD4 exome AF: 0.00286 AC: 4175AN: 1461544Hom.: 13 Cov.: 32 AF XY: 0.00282 AC XY: 2048AN XY: 727022
GnomAD4 genome AF: 0.00321 AC: 489AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00385 AC XY: 287AN XY: 74480
ClinVar
Submissions by phenotype
not provided Benign:4
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at