rs11187545

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_006744.4(RBP4):​c.355+3045T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0874 in 152,300 control chromosomes in the GnomAD database, including 730 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 0.087 ( 730 hom., cov: 32)

Consequence

RBP4
NM_006744.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.159

Publications

12 publications found
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]
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 was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
RBP4NM_006744.4 linkc.355+3045T>C intron_variant Intron 4 of 5 ENST00000371464.8 NP_006735.2 P02753
RBP4NM_001323517.1 linkc.355+3045T>C intron_variant Intron 4 of 5 NP_001310446.1 P02753
RBP4NM_001323518.2 linkc.349+3045T>C intron_variant Intron 4 of 5 NP_001310447.1 P02753Q5VY30

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
RBP4ENST00000371464.8 linkc.355+3045T>C intron_variant Intron 4 of 5 1 NM_006744.4 ENSP00000360519.3 P02753
FFAR4ENST00000604414.1 linkc.697-6726A>G intron_variant Intron 2 of 2 3 ENSP00000474477.1 S4R3L2
RBP4ENST00000371467.5 linkc.355+3045T>C intron_variant Intron 4 of 5 5 ENSP00000360522.1 P02753
RBP4ENST00000371469.2 linkc.349+3045T>C intron_variant Intron 4 of 5 5 ENSP00000360524.2 Q5VY30

Frequencies

GnomAD3 genomes
AF:
0.0873
AC:
13289
AN:
152182
Hom.:
728
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.125
Gnomad AMI
AF:
0.154
Gnomad AMR
AF:
0.0618
Gnomad ASJ
AF:
0.114
Gnomad EAS
AF:
0.00231
Gnomad SAS
AF:
0.0431
Gnomad FIN
AF:
0.0739
Gnomad MID
AF:
0.104
Gnomad NFE
AF:
0.0793
Gnomad OTH
AF:
0.0907
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0874
AC:
13308
AN:
152300
Hom.:
730
Cov.:
32
AF XY:
0.0852
AC XY:
6347
AN XY:
74474
show subpopulations
African (AFR)
AF:
0.125
AC:
5211
AN:
41550
American (AMR)
AF:
0.0617
AC:
944
AN:
15304
Ashkenazi Jewish (ASJ)
AF:
0.114
AC:
395
AN:
3470
East Asian (EAS)
AF:
0.00212
AC:
11
AN:
5184
South Asian (SAS)
AF:
0.0429
AC:
207
AN:
4826
European-Finnish (FIN)
AF:
0.0739
AC:
784
AN:
10616
Middle Eastern (MID)
AF:
0.112
AC:
33
AN:
294
European-Non Finnish (NFE)
AF:
0.0793
AC:
5393
AN:
68030
Other (OTH)
AF:
0.0898
AC:
190
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
624
1248
1871
2495
3119
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
144
288
432
576
720
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.0816
Hom.:
1427
Bravo
AF:
0.0878
Asia WGS
AF:
0.0370
AC:
129
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
4.6
DANN
Benign
0.75
PhyloP100
0.16
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.050
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs11187545; hg19: chr10-95357105; API