NM_000804.4:c.292C>T
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1
The NM_000804.4(FOLR3):c.292C>T(p.Arg98Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0477 in 1,594,208 control chromosomes in the GnomAD database, including 2,020 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/14 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Consequence
NM_000804.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOLR3 | ENST00000611028.3 | c.292C>T | p.Arg98Cys | missense_variant | Exon 3 of 5 | 1 | NM_000804.4 | ENSP00000481114.1 | ||
FOLR3 | ENST00000612844.4 | n.420C>T | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | ENSP00000481027.1 | ||||
FOLR3 | ENST00000622388.4 | c.292C>T | p.Arg98Cys | missense_variant | Exon 4 of 6 | 5 | ENSP00000481833.1 |
Frequencies
GnomAD3 genomes AF: 0.0404 AC: 5344AN: 132416Hom.: 125 Cov.: 33
GnomAD3 exomes AF: 0.0350 AC: 8787AN: 251052Hom.: 209 AF XY: 0.0360 AC XY: 4887AN XY: 135702
GnomAD4 exome AF: 0.0483 AC: 70635AN: 1461662Hom.: 1895 Cov.: 30 AF XY: 0.0478 AC XY: 34765AN XY: 727110
GnomAD4 genome AF: 0.0403 AC: 5343AN: 132546Hom.: 125 Cov.: 33 AF XY: 0.0393 AC XY: 2507AN XY: 63734
ClinVar
Submissions by phenotype
FOLR3-related disorder Benign:1
This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at