1-240092887-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_020066.5(FMN2):c.778G>A(p.Ala260Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0016 in 1,517,818 control chromosomes in the GnomAD database, including 37 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_020066.5 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: 0.00897 AC: 1365AN: 152102Hom.: 17 Cov.: 33
GnomAD3 exomes AF: 0.00218 AC: 242AN: 111134Hom.: 3 AF XY: 0.00192 AC XY: 116AN XY: 60556
GnomAD4 exome AF: 0.000770 AC: 1052AN: 1365602Hom.: 19 Cov.: 88 AF XY: 0.000678 AC XY: 456AN XY: 672450
GnomAD4 genome AF: 0.00903 AC: 1375AN: 152216Hom.: 18 Cov.: 33 AF XY: 0.00895 AC XY: 666AN XY: 74404
ClinVar
Submissions by phenotype
not provided Benign:3
Benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Dec 30, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at