3-139460011-T-C

Variant names:

• chr3-139460011-T-C
• rs2118981
• NM_004164.3:c.252+2101A>G

Variant summary

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

The NM_004164.3(RBP2):​c.252+2101A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.534 in 152,050 control chromosomes in the GnomAD database, including 24,655 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 0.53 (24655 hom., cov: 32)
• Consequence: RBP2 NM_004164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0490
• Publications: 6 publications found

Genes affected

RBP2 (HGNC:9920): (retinol binding protein 2) This gene encodes an abundant protein present in the small intestinal epithelium. It is thought to participate in the uptake and/or intracellular metabolism of vitamin A. Vitamin A is a fat-soluble vitamin necessary for growth, reproduction, differentiation of epithelial tissues, and vision. This protein may also modulate the supply of retinoic acid to the nuclei of endometrial cells during the menstrual cycle. [provided by RefSeq, Aug 2015]

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 = 0.9 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
RBP2	NM_004164.3	c.252+2101A>G		intron_variant	Intron 2 of 3	ENST00000232217.6	NP_004155.2
COPB2-DT	NR_121609.1	n.354+36897T>C		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
RBP2	ENST00000232217.6	c.252+2101A>G		intron_variant	Intron 2 of 3	1	NM_004164.3	ENSP00000232217.2

Frequencies

GnomAD3 genomes AF: 0.534 AC: 81151 AN: 151932 Hom.: 24598 Cov.: 32

Gnomad AFR AF: 0.785

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.615

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.923

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.491

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

GnomAD4 genome AF: 0.534 AC: 81266 AN: 152050 Hom.: 24655 Cov.: 32 AF XY: 0.534 AC XY: 39692 AN XY: 74330

African (AFR) AF: 0.785 AC: 32563 AN: 41484

American (AMR) AF: 0.616 AC: 9407 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.410 AC: 1423 AN: 3470

East Asian (EAS) AF: 0.922 AC: 4759 AN: 5160

South Asian (SAS) AF: 0.475 AC: 2291 AN: 4820

European-Finnish (FIN) AF: 0.306 AC: 3237 AN: 10572

Middle Eastern (MID) AF: 0.374 AC: 110 AN: 294

European-Non Finnish (NFE) AF: 0.386 AC: 26210 AN: 67962

Other (OTH) AF: 0.492 AC: 1038 AN: 2110

Alfa AF: 0.483 Hom.: 12677

Bravo AF: 0.575

Asia WGS AF: 0.686 AC: 2383 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	4.5
DANN	Benign	0.58
PhyloP100		-0.049
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: rs2118981; hg19: chr3-139178853;