3-139522529-C-T

Variant names:

• chr3-139522529-C-T
• rs295490
• NM_002899.5:c.439-4007G>A

Variant summary

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

The NM_002899.5(RBP1):​c.439-4007G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.787 in 152,072 control chromosomes in the GnomAD database, including 48,304 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 0.79 (48304 hom., cov: 31)
• Consequence: RBP1 NM_002899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.270
• Publications: 7 publications found

Genes affected

RBP1 (HGNC:9919): (retinol binding protein 1) This gene encodes the carrier protein involved in the transport of retinol (vitamin A alcohol) from the liver storage site to peripheral tissue. Vitamin A is a fat-soluble vitamin necessary for growth, reproduction, differentiation of epithelial tissues, and vision. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2008]

COPB2-DT (HGNC:55579): (COPB2 divergent transcript)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.915 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBP1	NM_002899.5	c.439-4007G>A		intron_variant	Intron 2 of 3	ENST00000672186.1	NP_002890.2
RBP1	NM_001365940.2	c.253-4007G>A		intron_variant	Intron 2 of 3		NP_001352869.1
COPB2-DT	NR_121609.1	n.355-55263C>T		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBP1	ENST00000672186.1	c.439-4007G>A		intron_variant	Intron 2 of 3		NM_002899.5	ENSP00000500931.1

Frequencies

GnomAD3 genomes AF: 0.787 AC: 119624 AN: 151954 Hom.: 48273 Cov.: 31

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.888

Gnomad AMR AF: 0.860

Gnomad ASJ AF: 0.795

Gnomad EAS AF: 0.937

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.870

Gnomad OTH AF: 0.795

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

GnomAD4 genome AF: 0.787 AC: 119712 AN: 152072 Hom.: 48304 Cov.: 31 AF XY: 0.788 AC XY: 58538 AN XY: 74318

African (AFR) AF: 0.591 AC: 24479 AN: 41450

American (AMR) AF: 0.860 AC: 13147 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.795 AC: 2761 AN: 3472

East Asian (EAS) AF: 0.937 AC: 4824 AN: 5148

South Asian (SAS) AF: 0.787 AC: 3790 AN: 4814

European-Finnish (FIN) AF: 0.837 AC: 8849 AN: 10576

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.870 AC: 59159 AN: 68020

Other (OTH) AF: 0.794 AC: 1671 AN: 2104

Alfa AF: 0.813 Hom.: 17676

Bravo AF: 0.784

Asia WGS AF: 0.830 AC: 2889 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.2
DANN	Benign	0.71
PhyloP100		-0.27
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: rs295490; hg19: chr3-139241371;