chr3-139476062-A-G

Variant names:

• chr3-139476062-A-G
• rs35674260
• NM_004164.3:c.73+325T>C

Variant summary

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

The NM_004164.3(RBP2):​c.73+325T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.627 in 152,126 control chromosomes in the GnomAD database, including 32,675 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 0.63 (32675 hom., cov: 32)
• Consequence: RBP2 NM_004164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.934 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_004164.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP2	NM_004164.3	MANE Select	c.73+325T>C		intron	N/A	NP_004155.2
	COPB2-DT	NR_121609.1		n.354+52948A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP2	ENST00000232217.6	TSL:1 MANE Select	c.73+325T>C		intron	N/A	ENSP00000232217.2	P50120
	RBP2	ENST00000950403.1		c.73+325T>C		intron	N/A	ENSP00000620462.1
	RBP2	ENST00000511956.1	TSL:3	c.73+325T>C		intron	N/A	ENSP00000424333.1	D6RB89

Frequencies

GnomAD3 genomes AF: 0.627 AC: 95332 AN: 152006 Hom.: 32613 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.685

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.957

Gnomad SAS AF: 0.591

Gnomad FIN AF: 0.461

Gnomad MID AF: 0.525

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.627 AC: 95450 AN: 152126 Hom.: 32675 Cov.: 32 AF XY: 0.631 AC XY: 46886 AN XY: 74360

African (AFR) AF: 0.883 AC: 36706 AN: 41558

American (AMR) AF: 0.686 AC: 10474 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3466

East Asian (EAS) AF: 0.956 AC: 4934 AN: 5162

South Asian (SAS) AF: 0.589 AC: 2840 AN: 4822

European-Finnish (FIN) AF: 0.461 AC: 4871 AN: 10570

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32191 AN: 67962

Other (OTH) AF: 0.592 AC: 1249 AN: 2110

Alfa AF: 0.585 Hom.: 4872

Bravo AF: 0.660

Asia WGS AF: 0.762 AC: 2645 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.040
DANN	Benign	0.54
PhyloP100		-1.8
PromoterAI		0.0072	Neutral
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: rs35674260; hg19: chr3-139194904;