11-72139110-CTA-C
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_000804.4(FOLR3):c.320_321delAT(p.Tyr107fs) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.918 in 1,613,676 control chromosomes in the GnomAD database, including 681,325 homozygotes. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: 𝑓 0.87 ( 58449 hom., cov: 0)
Exomes 𝑓: 0.92 ( 622876 hom. )
Consequence
FOLR3
NM_000804.4 frameshift
NM_000804.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 7.80
Genes affected
FOLR3 (HGNC:3795): (folate receptor gamma) This gene encodes a member of the folate receptor (FOLR) family of proteins, which have a high affinity for folic acid and for several reduced folic acid derivatives, and mediate delivery of 5-methyltetrahydrofolate to the interior of cells. Expression of this gene may be elevated in ovarian and primary peritoneal carcinoma. This gene is present in a gene cluster on chromosome 11. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2015]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
Variant 11-72139110-CTA-C is Benign according to our data. Variant chr11-72139110-CTA-C is described in ClinVar as [Benign]. Clinvar id is 768461.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.928 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOLR3 | ENST00000611028.3 | c.320_321delAT | p.Tyr107fs | frameshift_variant | Exon 3 of 5 | 1 | NM_000804.4 | ENSP00000481114.1 | ||
FOLR3 | ENST00000612844.4 | n.448_449delAT | non_coding_transcript_exon_variant | Exon 3 of 5 | 1 | ENSP00000481027.1 | ||||
FOLR3 | ENST00000622388.4 | c.320_321delAT | p.Tyr107fs | frameshift_variant | Exon 4 of 6 | 5 | ENSP00000481833.1 |
Frequencies
GnomAD3 genomes AF: 0.873 AC: 132711AN: 151980Hom.: 58426 Cov.: 0
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GnomAD4 exome AF: 0.923 AC: 1348482AN: 1461578Hom.: 622876 AF XY: 0.924 AC XY: 671815AN XY: 727058
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GnomAD4 genome AF: 0.873 AC: 132773AN: 152098Hom.: 58449 Cov.: 0 AF XY: 0.873 AC XY: 64910AN XY: 74364
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
Computational scores
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Find out detailed SpliceAI scores and Pangolin per-transcript scores at