rs11187548
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_006744.4(RBP4):c.355+212G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.034 in 152,206 control chromosomes in the GnomAD database, including 295 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.034 ( 295 hom., cov: 32)
Consequence
RBP4
NM_006744.4 intron
NM_006744.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.261
Genes affected
RBP4 (HGNC:9922): (retinol binding protein 4) This protein belongs to the lipocalin family and is the specific carrier for retinol (vitamin A alcohol) in the blood. It delivers retinol from the liver stores to the peripheral tissues. In plasma, the RBP-retinol complex interacts with transthyretin which prevents its loss by filtration through the kidney glomeruli. A deficiency of vitamin A blocks secretion of the binding protein posttranslationally and results in defective delivery and supply to the epidermal cells. [provided by RefSeq, Jul 2008]
FFAR4 (HGNC:19061): (free fatty acid receptor 4) This gene encodes a G protein-coupled receptor (GPR) which belongs to the rhodopsin family of GPRs. The encoded protein functions as a receptor for free fatty acids, including omega-3, and participates in suppressing anti-inflammatory responses and insulin sensitizing. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]
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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=-0.81).
BP6
?
Variant 10-93600181-C-T is Benign according to our data. Variant chr10-93600181-C-T is described in ClinVar as [Benign]. Clinvar id is 1261690.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.114 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RBP4 | NM_006744.4 | c.355+212G>A | intron_variant | ENST00000371464.8 | |||
RBP4 | NM_001323517.1 | c.355+212G>A | intron_variant | ||||
RBP4 | NM_001323518.2 | c.349+212G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RBP4 | ENST00000371464.8 | c.355+212G>A | intron_variant | 1 | NM_006744.4 | P1 | |||
RBP4 | ENST00000371467.5 | c.355+212G>A | intron_variant | 5 | P1 | ||||
RBP4 | ENST00000371469.2 | c.349+212G>A | intron_variant | 5 | |||||
FFAR4 | ENST00000604414.1 | c.697-3893C>T | intron_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0340 AC: 5164AN: 152088Hom.: 296 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: 0.0340 AC: 5176AN: 152206Hom.: 295 Cov.: 32 AF XY: 0.0329 AC XY: 2448AN XY: 74428
GnomAD4 genome
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2448
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74428
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3478
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 | May 16, 2021 | - - |
Computational scores
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Name
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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