1-11858387-C-T
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The NM_002521.3(NPPB):c.215G>A(p.Arg72His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00171 in 1,598,676 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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: 0.00277 AC: 421AN: 152148Hom.: 4 Cov.: 32
GnomAD3 exomes AF: 0.00364 AC: 862AN: 236984Hom.: 13 AF XY: 0.00358 AC XY: 458AN XY: 128106
GnomAD4 exome AF: 0.00160 AC: 2313AN: 1446410Hom.: 35 Cov.: 32 AF XY: 0.00155 AC XY: 1109AN XY: 717710
GnomAD4 genome AF: 0.00276 AC: 421AN: 152266Hom.: 4 Cov.: 32 AF XY: 0.00379 AC XY: 282AN XY: 74444
ClinVar
Submissions by phenotype
not provided Benign:2
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at