10-70255663-C-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_022146.5(NPFFR1):c.587G>T(p.Arg196Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00185 in 1,598,312 control chromosomes in the GnomAD database, including 41 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_022146.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00802 AC: 1221AN: 152160Hom.: 16 Cov.: 32
GnomAD3 exomes AF: 0.00217 AC: 473AN: 217896Hom.: 8 AF XY: 0.00152 AC XY: 180AN XY: 118532
GnomAD4 exome AF: 0.00120 AC: 1739AN: 1446034Hom.: 25 Cov.: 37 AF XY: 0.00104 AC XY: 750AN XY: 717706
GnomAD4 genome AF: 0.00803 AC: 1223AN: 152278Hom.: 16 Cov.: 32 AF XY: 0.00766 AC XY: 570AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Mar 07, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at