chr11-86945858-GAA-G
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBS1BS2
The NM_012193.4(FZD4):c.*5282_*5283del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0034 in 152,238 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0034 ( 2 hom., cov: 32)
Consequence
FZD4
NM_012193.4 3_prime_UTR
NM_012193.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.24
Genes affected
FZD4 (HGNC:4042): (frizzled class receptor 4) This gene is a member of the frizzled gene family. Members of this family encode seven-transmembrane domain proteins that are receptors for the Wingless type MMTV integration site family of signaling proteins. Most frizzled receptors are coupled to the beta-catenin canonical signaling pathway. This protein may play a role as a positive regulator of the Wingless type MMTV integration site signaling pathway. A transcript variant retaining intronic sequence and encoding a shorter isoform has been described, however, its expression is not supported by other experimental evidence. [provided by RefSeq, Jul 2008]
PRSS23 (HGNC:14370): (serine protease 23) This gene encodes a conserved member of the trypsin family of serine proteases. Mouse studies found a decrease of mRNA levels of this gene after ovulation was induced. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP6
?
Variant 11-86945858-GAA-G is Benign according to our data. Variant chr11-86945858-GAA-G is described in ClinVar as [Likely_benign]. Clinvar id is 306327.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0034 (518/152238) while in subpopulation AFR AF= 0.012 (497/41528). AF 95% confidence interval is 0.0111. There are 2 homozygotes in gnomad4. There are 231 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
?
High AC in GnomAd at 518 AD,Digenic gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FZD4 | NM_012193.4 | c.*5282_*5283del | 3_prime_UTR_variant | 2/2 | ENST00000531380.2 | ||
PRSS23 | NR_120591.3 | n.435-4497_435-4496del | intron_variant, non_coding_transcript_variant | ||||
PRSS23 | NR_120592.2 | n.328-5357_328-5356del | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FZD4 | ENST00000531380.2 | c.*5282_*5283del | 3_prime_UTR_variant | 2/2 | 1 | NM_012193.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00341 AC: 518AN: 152120Hom.: 2 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.00340 AC: 518AN: 152238Hom.: 2 Cov.: 32 AF XY: 0.00310 AC XY: 231AN XY: 74436
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Familial exudative vitreoretinopathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
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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