rs17484721

Positions:

• chr10-93593555-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006744.4(RBP4):​c.568+268T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 151,928 control chromosomes in the GnomAD database, including 1,955 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1955 hom., cov: 32)
• Consequence: RBP4 NM_006744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.14

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBP4	NM_006744.4	c.568+268T>C		intron_variant		ENST00000371464.8	NP_006735.2
RBP4	NM_001323517.1	c.568+268T>C		intron_variant			NP_001310446.1
RBP4	NM_001323518.2	c.562+268T>C		intron_variant			NP_001310447.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBP4	ENST00000371464.8	c.568+268T>C		intron_variant		1	NM_006744.4	ENSP00000360519	P1
RBP4	ENST00000371467.5	c.568+268T>C		intron_variant		5		ENSP00000360522	P1
RBP4	ENST00000371469.2	c.562+268T>C		intron_variant		5		ENSP00000360524
FFAR4	ENST00000604414.1	c.697-10519A>G		intron_variant		3		ENSP00000474477

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22776 AN: 151810 Hom.: 1957 Cov.: 32

Gnomad AFR AF: 0.0816

Gnomad AMI AF: 0.0626

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.160

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.173

Gnomad OTH AF: 0.190

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

GnomAD4 genome AF: 0.150 AC: 22797 AN: 151928 Hom.: 1955 Cov.: 32 AF XY: 0.154 AC XY: 11462 AN XY: 74244

Gnomad4 AFR AF: 0.0816

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.239

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.160

Gnomad4 NFE AF: 0.173

Gnomad4 OTH AF: 0.188

Alfa AF: 0.153 Hom.: 259

Bravo AF: 0.145

Asia WGS AF: 0.187 AC: 649 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.024
DANN	Benign	0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17484721; hg19: chr10-95353312;