10-93593803-G-A
Variant names:
Variant summary
Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_006744.4(RBP4):c.568+20C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000302 in 1,456,808 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.000030 ( 0 hom. )
Consequence
RBP4
NM_006744.4 intron
NM_006744.4 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.238
Publications
0 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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BP6
Variant 10-93593803-G-A is Benign according to our data. Variant chr10-93593803-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 3680584.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population nfe. GnomAdExome4 allele frequency = 0.0000302 (44/1456808) while in subpopulation NFE AF = 0.0000396 (44/1110474). AF 95% confidence interval is 0.00003. There are 0 homozygotes in GnomAdExome4. There are 19 alleles in the male GnomAdExome4 subpopulation. Median coverage is 32. This position passed quality control check.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RBP4 | NM_006744.4 | c.568+20C>T | intron_variant | Intron 5 of 5 | ENST00000371464.8 | NP_006735.2 | ||
RBP4 | NM_001323517.1 | c.568+20C>T | intron_variant | Intron 5 of 5 | NP_001310446.1 | |||
RBP4 | NM_001323518.2 | c.562+20C>T | intron_variant | Intron 5 of 5 | NP_001310447.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RBP4 | ENST00000371464.8 | c.568+20C>T | intron_variant | Intron 5 of 5 | 1 | NM_006744.4 | ENSP00000360519.3 | |||
FFAR4 | ENST00000604414.1 | c.697-10271G>A | intron_variant | Intron 2 of 2 | 3 | ENSP00000474477.1 | ||||
RBP4 | ENST00000371467.5 | c.568+20C>T | intron_variant | Intron 5 of 5 | 5 | ENSP00000360522.1 | ||||
RBP4 | ENST00000371469.2 | c.562+20C>T | intron_variant | Intron 5 of 5 | 5 | ENSP00000360524.2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000401 AC: 1AN: 249670 AF XY: 0.00000740 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
249670
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.0000302 AC: 44AN: 1456808Hom.: 0 Cov.: 32 AF XY: 0.0000262 AC XY: 19AN XY: 724908 show subpopulations
GnomAD4 exome
AF:
AC:
44
AN:
1456808
Hom.:
Cov.:
32
AF XY:
AC XY:
19
AN XY:
724908
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33388
American (AMR)
AF:
AC:
0
AN:
44708
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26118
East Asian (EAS)
AF:
AC:
0
AN:
39690
South Asian (SAS)
AF:
AC:
0
AN:
86134
European-Finnish (FIN)
AF:
AC:
0
AN:
51988
Middle Eastern (MID)
AF:
AC:
0
AN:
4162
European-Non Finnish (NFE)
AF:
AC:
44
AN:
1110474
Other (OTH)
AF:
AC:
0
AN:
60146
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.477
Heterozygous variant carriers
0
3
6
10
13
16
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Apr 08, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance:Likely benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing
- -
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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