rs10882280

Variant names:

• chr10-93599556-C-A
• rs10882280
• NM_006744.4:c.355+837G>T

Your query was ambiguous. Multiple possible variants found:

• chr10-93599556-C-A
• chr10-93599556-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_006744.4(RBP4):​c.355+837G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.081 in 152,228 control chromosomes in the GnomAD database, including 612 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 0.081 (612 hom., cov: 32)
• Consequence: RBP4 NM_006744.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.10
• Publications: 10 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.102 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006744.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP4	NM_006744.4	MANE Select	c.355+837G>T		intron	N/A	NP_006735.2
	RBP4	NM_001323517.1		c.355+837G>T		intron	N/A	NP_001310446.1
	RBP4	NM_001323518.2		c.349+837G>T		intron	N/A	NP_001310447.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP4	ENST00000371464.8	TSL:1 MANE Select	c.355+837G>T		intron	N/A	ENSP00000360519.3
	FFAR4	ENST00000604414.1	TSL:3	c.697-4518C>A		intron	N/A	ENSP00000474477.1
	RBP4	ENST00000371467.5	TSL:5	c.355+837G>T		intron	N/A	ENSP00000360522.1

Frequencies

GnomAD3 genomes AF: 0.0809 AC: 12309 AN: 152110 Hom.: 611 Cov.: 32

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0597

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.00232

Gnomad SAS AF: 0.0421

Gnomad FIN AF: 0.0739

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.0786

Gnomad OTH AF: 0.0871

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

GnomAD4 genome AF: 0.0810 AC: 12325 AN: 152228 Hom.: 612 Cov.: 32 AF XY: 0.0789 AC XY: 5869 AN XY: 74424

African (AFR) AF: 0.105 AC: 4346 AN: 41532

American (AMR) AF: 0.0596 AC: 912 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.107 AC: 370 AN: 3470

East Asian (EAS) AF: 0.00213 AC: 11 AN: 5170

South Asian (SAS) AF: 0.0421 AC: 203 AN: 4820

European-Finnish (FIN) AF: 0.0739 AC: 784 AN: 10610

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0786 AC: 5344 AN: 68012

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0845 Hom.: 118

Bravo AF: 0.0802

Asia WGS AF: 0.0360 AC: 127 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	12
DANN	Benign	0.81
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10882280; hg19: chr10-95359313;