11-119344061-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
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
Publications
9 publications found
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]
C1QTNF5 (HGNC:14344): (C1q and TNF related 5) This gene encodes a member of a family of proteins that function as components of basement membranes and may play a role in cell adhesion. Mutations in this gene have been associated with late-onset retinal degeneration. The protein may be encoded by either a bicistronic transcript including sequence from the upstream membrane frizzled-related protein gene (MFRP), or by a monocistronic transcript expressed from an internal promoter. [provided by RefSeq, Jun 2013]
C1QTNF5 Gene-Disease associations (from GenCC):
- late-onset retinal degenerationInheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae), G2P
Genome browser will be placed here
ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -20 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_multiple_submitters_no_conflicts, 2 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MFRP | NM_031433.4 | c.976-97T>C | intron_variant | Intron 8 of 14 | ENST00000619721.6 | NP_113621.1 | ||
C1QTNF5 | NM_015645.5 | c.-1661-97T>C | intron_variant | Intron 8 of 14 | NP_056460.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.490 AC: 74083AN: 151212Hom.: 19808 Cov.: 29 show subpopulations
GnomAD3 genomes
AF:
AC:
74083
AN:
151212
Hom.:
Cov.:
29
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.577 AC: 777904AN: 1347544Hom.: 228462 AF XY: 0.579 AC XY: 390923AN XY: 674898 show subpopulations
GnomAD4 exome
AF:
AC:
777904
AN:
1347544
Hom.:
AF XY:
AC XY:
390923
AN XY:
674898
show subpopulations
African (AFR)
AF:
AC:
7646
AN:
31506
American (AMR)
AF:
AC:
25944
AN:
42436
Ashkenazi Jewish (ASJ)
AF:
AC:
11653
AN:
25234
East Asian (EAS)
AF:
AC:
12948
AN:
38930
South Asian (SAS)
AF:
AC:
51964
AN:
82720
European-Finnish (FIN)
AF:
AC:
24967
AN:
40888
Middle Eastern (MID)
AF:
AC:
2515
AN:
5188
European-Non Finnish (NFE)
AF:
AC:
609155
AN:
1023836
Other (OTH)
AF:
AC:
31112
AN:
56806
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
17307
34614
51920
69227
86534
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Exome Hom
Variant carriers
0
16056
32112
48168
64224
80280
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome AF: 0.489 AC: 74070AN: 151332Hom.: 19797 Cov.: 29 AF XY: 0.495 AC XY: 36553AN XY: 73910 show subpopulations
GnomAD4 genome
AF:
AC:
74070
AN:
151332
Hom.:
Cov.:
29
AF XY:
AC XY:
36553
AN XY:
73910
show subpopulations
African (AFR)
AF:
AC:
10964
AN:
41126
American (AMR)
AF:
AC:
8678
AN:
15228
Ashkenazi Jewish (ASJ)
AF:
AC:
1619
AN:
3462
East Asian (EAS)
AF:
AC:
1532
AN:
5090
South Asian (SAS)
AF:
AC:
3067
AN:
4786
European-Finnish (FIN)
AF:
AC:
6552
AN:
10486
Middle Eastern (MID)
AF:
AC:
145
AN:
294
European-Non Finnish (NFE)
AF:
AC:
40011
AN:
67854
Other (OTH)
AF:
AC:
1050
AN:
2098
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.506
Heterozygous variant carriers
0
1748
3496
5243
6991
8739
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
658
1316
1974
2632
3290
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
-
Breakthrough Genomics, Breakthrough Genomics
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:not provided
- -
Nov 12, 2018
GeneDx
Significance: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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