rs1221189280
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_016729.3(FOLR1):c.169-8C>A variant causes a splice region, splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 33)
Consequence
FOLR1
NM_016729.3 splice_region, splice_polypyrimidine_tract, intron
NM_016729.3 splice_region, splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.0002526
2
Clinical Significance
Conservation
PhyloP100: 0.0200
Genes affected
FOLR1 (HGNC:3791): (folate receptor alpha) The protein encoded by this gene is a member of the folate receptor family. Members of this gene family bind folic acid and its reduced derivatives, and transport 5-methyltetrahydrofolate into cells. This gene product is a secreted protein that either anchors to membranes via a glycosyl-phosphatidylinositol linkage or exists in a soluble form. Mutations in this gene have been associated with neurodegeneration due to cerebral folate transport deficiency. Due to the presence of two promoters, multiple transcription start sites, and alternative splicing, multiple transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Oct 2009]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.79).
BP6
?
Variant 11-72195263-C-A is Benign according to our data. Variant chr11-72195263-C-A is described in ClinVar as [Likely_benign]. Clinvar id is 470722.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FOLR1 | NM_016729.3 | c.169-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ENST00000393676.5 | |||
FOLR1 | NM_000802.3 | c.169-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
FOLR1 | NM_016724.3 | c.169-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | ||||
FOLR1 | NM_016725.3 | c.169-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FOLR1 | ENST00000393676.5 | c.169-8C>A | splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_016729.3 | P1 | |||
ENST00000378140.3 | n.419+3250G>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Cerebral folate transport deficiency Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Feb 29, 2020 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at