rs883245
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_031433.4(MFRP):c.-88C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.528 in 1,374,554 control chromosomes in the GnomAD database, including 193,737 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.50 ( 19730 hom., cov: 32)
Exomes 𝑓: 0.53 ( 174007 hom. )
Consequence
MFRP
NM_031433.4 5_prime_UTR
NM_031433.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.252
Genes affected
MFRP (HGNC:18121): (membrane frizzled-related protein) This gene encodes a member of the frizzled-related protein family. The encoded protein plays an important role in eye development and mutations in this gene have been associated with nanophthalmos, posterior microphthalmia, retinitis pigmentosa, foveoschisis, and optic disc drusen. The protein is encoded by a bicistronic transcript which also encodes C1q and tumor necrosis factor related protein 5 (C1QTNF5). [provided by RefSeq, Jun 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
Variant 11-119346601-G-A is Benign according to our data. Variant chr11-119346601-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 302987.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-119346601-G-A is described in Lovd as [Benign].
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFRP | NM_031433.4 | c.-88C>T | 5_prime_UTR_variant | 1/15 | ENST00000619721.6 | ||
C1QTNF5 | NM_015645.5 | c.-2724C>T | 5_prime_UTR_variant | 1/15 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFRP | ENST00000619721.6 | c.-88C>T | 5_prime_UTR_variant | 1/15 | 1 | NM_031433.4 | P1 | ||
MFRP | ENST00000360167.4 | c.-88C>T | 5_prime_UTR_variant | 1/10 | 2 | ||||
MFRP | ENST00000526059.1 | n.17C>T | non_coding_transcript_exon_variant | 1/3 | 3 | ||||
MFRP | ENST00000634542.1 | c.-88C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/5 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.504 AC: 76536AN: 151878Hom.: 19709 Cov.: 32
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GnomAD4 exome AF: 0.531 AC: 649581AN: 1222558Hom.: 174007 Cov.: 17 AF XY: 0.535 AC XY: 331155AN XY: 618652
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GnomAD4 genome ? AF: 0.504 AC: 76600AN: 151996Hom.: 19730 Cov.: 32 AF XY: 0.510 AC XY: 37858AN XY: 74282
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Isolated microphthalmia 6 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Retinal degeneration Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at