chr11-72139110-C-CTA
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_000804.4(FOLR3):c.320_321dup(p.Glu108MetfsTer24) variant causes a frameshift change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Benign (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 0)
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 Likely_benign. Variant got -6 ACMG points.
BP6
?
Variant 11-72139110-C-CTA is Benign according to our data. Variant chr11-72139110-C-CTA is described in ClinVar as [Benign]. Clinvar id is 3035533.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome at 1167 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOLR3 | NM_000804.4 | c.320_321dup | p.Glu108MetfsTer24 | frameshift_variant | 3/5 | ENST00000611028.3 | |
FOLR3 | NR_178088.1 | n.498_499dup | non_coding_transcript_exon_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOLR3 | ENST00000611028.3 | c.320_321dup | p.Glu108MetfsTer24 | frameshift_variant | 3/5 | 1 | NM_000804.4 | P1 | |
FOLR3 | ENST00000612844.4 | c.448_449dup | p.Met150IlefsTer2 | frameshift_variant, NMD_transcript_variant | 3/5 | 1 | |||
FOLR3 | ENST00000622388.4 | c.320_321dup | p.Glu108MetfsTer24 | frameshift_variant | 4/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 0
GnomAD3 genomes
?
Cov.:
0
GnomAD3 exomes AF: 0.0829 AC: 20748AN: 250286Hom.: 1167 AF XY: 0.0792 AC XY: 10729AN XY: 135428
GnomAD3 exomes
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20748
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250286
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10729
AN XY:
135428
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GnomAD4 exome Cov.: 0
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GnomAD4 genome ? Cov.: 0
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0
Asia WGS
AF:
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281
AN:
3478
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FOLR3-related disorder Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 25, 2019 | 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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at