3-139522529-C-T

Position:

• chr3-139522529-C-T

Variant summary

Our verdict is Benign. Variant got -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

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]

RBP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
RBP1	NM_002899.5	c.439-4007G>A		intron_variant		ENST00000672186.1	NP_002890.2
RBP1	NM_001365940.2	c.253-4007G>A		intron_variant			NP_001352869.1
COPB2-DT	NR_121609.1	n.355-55263C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBP1	ENST00000672186.1	c.439-4007G>A		intron_variant			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

Gnomad4 AFR AF: 0.591

Gnomad4 AMR AF: 0.860

Gnomad4 ASJ AF: 0.795

Gnomad4 EAS AF: 0.937

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.870

Gnomad4 OTH AF: 0.794

Alfa AF: 0.799 Hom.: 8702

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

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: rs295490; hg19: chr3-139241371;