rs150393409
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_014967.5(FAN1):c.1520G>A(p.Arg507His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0089 in 1,614,058 control chromosomes in the GnomAD database, including 86 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_014967.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00605 AC: 920AN: 152090Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.00656 AC: 1649AN: 251456Hom.: 11 AF XY: 0.00684 AC XY: 930AN XY: 135908
GnomAD4 exome AF: 0.00920 AC: 13449AN: 1461850Hom.: 82 Cov.: 32 AF XY: 0.00906 AC XY: 6589AN XY: 727228
GnomAD4 genome AF: 0.00604 AC: 920AN: 152208Hom.: 4 Cov.: 33 AF XY: 0.00543 AC XY: 404AN XY: 74412
ClinVar
Submissions by phenotype
not provided Benign:2
- -
FAN1: BP4, BS2 -
Karyomegalic interstitial nephritis Uncertain:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at