11-119344061-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_031433.4(MFRP):c.976-97T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.568 in 1,498,876 control chromosomes in the GnomAD database, including 248,259 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.49 ( 19797 hom., cov: 29)
Exomes 𝑓: 0.58 ( 228462 hom. )
Consequence
MFRP
NM_031433.4 intron
NM_031433.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.06
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 -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 11-119344061-A-G is Benign according to our data. Variant chr11-119344061-A-G is described in ClinVar as [Benign]. Clinvar id is 1229543.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MFRP | NM_031433.4 | c.976-97T>C | intron_variant | ENST00000619721.6 | |||
C1QTNF5 | NM_015645.5 | c.-1661-97T>C | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MFRP | ENST00000619721.6 | c.976-97T>C | intron_variant | 1 | NM_031433.4 | P1 | |||
MFRP | ENST00000360167.4 | c.898+571T>C | intron_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.490 AC: 74083AN: 151212Hom.: 19808 Cov.: 29
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GnomAD4 exome AF: 0.577 AC: 777904AN: 1347544Hom.: 228462 AF XY: 0.579 AC XY: 390923AN XY: 674898
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GnomAD4 genome ? AF: 0.489 AC: 74070AN: 151332Hom.: 19797 Cov.: 29 AF XY: 0.495 AC XY: 36553AN XY: 73910
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at