11-72138993-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_000804.4(FOLR3):c.201G>A(p.Thr67=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00015 in 1,613,956 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. T67T) has been classified as Benign.
Frequency
Consequence
NM_000804.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOLR3 | NM_000804.4 | c.201G>A | p.Thr67= | synonymous_variant | 3/5 | ENST00000611028.3 | |
FOLR3 | NR_178088.1 | n.379G>A | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOLR3 | ENST00000611028.3 | c.201G>A | p.Thr67= | synonymous_variant | 3/5 | 1 | NM_000804.4 | P1 | |
FOLR3 | ENST00000612844.4 | c.329G>A | p.Arg110Gln | missense_variant, NMD_transcript_variant | 3/5 | 1 | |||
FOLR3 | ENST00000622388.4 | c.201G>A | p.Thr67= | synonymous_variant | 4/6 | 5 | |||
FOLR3 | ENST00000546166.1 | c.195G>A | p.Thr65= | synonymous_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000423 AC: 106AN: 250844Hom.: 1 AF XY: 0.000457 AC XY: 62AN XY: 135594
GnomAD4 exome AF: 0.000146 AC: 213AN: 1461698Hom.: 1 Cov.: 29 AF XY: 0.000166 AC XY: 121AN XY: 727136
GnomAD4 genome ? AF: 0.000190 AC: 29AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74446
ClinVar
Submissions by phenotype
FOLR3-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 09, 2020 | This variant is classified as likely 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