11-72135924-CTCTGACTGTGGCTCTCTGGCAGGAATAGATGGACA-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PVS1_StrongBP6BS2
The NM_000804.4(FOLR3):c.-6-21_8delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT variant causes a splice acceptor, 5 prime UTR truncation, exon loss, splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.003 in 152,198 control chromosomes in the GnomAD database, including 3 homozygotes. Variant has been reported in ClinVar as Likely benign (no stars).
Frequency
Consequence
NM_000804.4 splice_acceptor, 5_prime_UTR_truncation, exon_loss, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOLR3 | NM_000804.4 | c.-6-21_8delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT | p.Met1fs | frameshift_variant, start_lost, splice_region_variant | Exon 2 of 5 | ENST00000611028.3 | NP_000795.2 | |
FOLR3 | NM_000804.4 | c.-6-21_8delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT | splice_acceptor_variant, 5_prime_UTR_truncation, exon_loss_variant, splice_region_variant, intron_variant | Exon 2 of 5 | ENST00000611028.3 | NP_000795.2 | ||
FOLR3 | NR_178088.1 | n.45-21_58delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT | splice_acceptor_variant, splice_region_variant, intron_variant, non_coding_transcript_exon_variant | Exon 2 of 5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FOLR3 | ENST00000611028.3 | c.-6-21_8delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT | p.Met1fs | frameshift_variant, start_lost, splice_region_variant | Exon 2 of 5 | 1 | NM_000804.4 | ENSP00000481114.1 | ||
FOLR3 | ENST00000611028 | c.-6-21_8delCTGACTGTGGCTCTCTGGCAGGAATAGATGGACAT | splice_acceptor_variant, 5_prime_UTR_truncation, exon_loss_variant, splice_region_variant, intron_variant | Exon 2 of 5 | 1 | NM_000804.4 | ENSP00000481114.1 |
Frequencies
GnomAD3 genomes AF: 0.00299 AC: 455AN: 152082Hom.: 3 Cov.: 31
GnomAD3 exomes AF: 0.00100 AC: 248AN: 247764Hom.: 1 AF XY: 0.000803 AC XY: 108AN XY: 134420
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00150 AC: 2192AN: 1460424Hom.: 1 AF XY: 0.00142 AC XY: 1031AN XY: 726564
GnomAD4 genome AF: 0.00300 AC: 457AN: 152198Hom.: 3 Cov.: 31 AF XY: 0.00285 AC XY: 212AN XY: 74424
ClinVar
Submissions by phenotype
FOLR3-related disorder Benign:1
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