Variant chr10-93593485-C-CA details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_006744.4(RBP4):c.568+337_568+338insT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 28)

Consequence

RBP4
NM_006744.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.407

Variant links:

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]

RBP4 links:

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]

FFAR4 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
RBP4	NM_006744.4 linkuse as main transcript	c.568+337_568+338insT	intron_variant	ENST00000371464.8	NP_006735.2
RBP4	NM_001323517.1 linkuse as main transcript	c.568+337_568+338insT	intron_variant		NP_001310446.1
RBP4	NM_001323518.2 linkuse as main transcript	c.562+337_562+338insT	intron_variant		NP_001310447.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
RBP4	ENST00000371464.8 linkuse as main transcript	c.568+337_568+338insT	intron_variant	1	NM_006744.4	ENSP00000360519	P1
RBP4	ENST00000371467.5 linkuse as main transcript	c.568+337_568+338insT	intron_variant	5		ENSP00000360522	P1
RBP4	ENST00000371469.2 linkuse as main transcript	c.562+337_562+338insT	intron_variant	5		ENSP00000360524
FFAR4	ENST00000604414.1 linkuse as main transcript	c.697-10587dup	intron_variant	3		ENSP00000474477

Frequencies

GnomAD3 genomes

Cov.:

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing