chr11-72196045-C-T
Variant names:
Variant summary
Our verdict is Benign. The variant received -9 ACMG points: 2P and 11B. PM2BP4_ModerateBP6_Very_StrongBP7
The NM_016729.3(FOLR1):c.642C>T(p.Phe214Phe) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
FOLR1
NM_016729.3 synonymous
NM_016729.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.93
Publications
2 publications found
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]
FOLR1 Gene-Disease associations (from GenCC):
- neurodegenerative syndrome due to cerebral folate transport deficiencyInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: ClinGen, Laboratory for Molecular Medicine, Labcorp Genetics (formerly Invitae), Orphanet, G2P
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -9 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.34).
BP6
Variant 11-72196045-C-T is Benign according to our data. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-72196045-C-T is described in CliVar as Likely_benign. Clinvar id is 470725.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
Synonymous conserved (PhyloP=-1.93 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FOLR1 | NM_016729.3 | c.642C>T | p.Phe214Phe | synonymous_variant | Exon 4 of 4 | ENST00000393676.5 | NP_057941.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
152208
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
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Gnomad FIN
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Gnomad MID
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Gnomad OTH
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GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251422 AF XY: 0.00000736 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251422
AF XY:
Gnomad AFR exome
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GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461894Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727248 show subpopulations
GnomAD4 exome
AF:
AC:
3
AN:
1461894
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
727248
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33480
American (AMR)
AF:
AC:
0
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
1
AN:
39700
South Asian (SAS)
AF:
AC:
1
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53420
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1112012
Other (OTH)
AF:
AC:
1
AN:
60396
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.458
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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<30
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65-70
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>80
Age
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152208Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356 show subpopulations
GnomAD4 genome
AF:
AC:
1
AN:
152208
Hom.:
Cov.:
33
AF XY:
AC XY:
1
AN XY:
74356
show subpopulations
African (AFR)
AF:
AC:
1
AN:
41456
American (AMR)
AF:
AC:
0
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
3472
East Asian (EAS)
AF:
AC:
0
AN:
5202
South Asian (SAS)
AF:
AC:
0
AN:
4838
European-Finnish (FIN)
AF:
AC:
0
AN:
10612
Middle Eastern (MID)
AF:
AC:
0
AN:
316
European-Non Finnish (NFE)
AF:
AC:
0
AN:
68028
Other (OTH)
AF:
AC:
0
AN:
2090
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.425
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Likely benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:1
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Cerebral folate transport deficiency Benign:1
Aug 17, 2023
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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