rs16849083

Variant names:

• chr3-139465437-C-T
• rs16849083
• NM_004164.3:c.74-3147G>A

Variant summary

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

The NM_004164.3(RBP2):​c.74-3147G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 152,116 control chromosomes in the GnomAD database, including 1,998 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 0.11 (1998 hom., cov: 32)
• Consequence: RBP2 NM_004164.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.493
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.289 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP2	NM_004164.3	MANE Select	c.74-3147G>A		intron	N/A	NP_004155.2
	COPB2-DT	NR_121609.1		n.354+42323C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP2	ENST00000232217.6	TSL:1 MANE Select	c.74-3147G>A		intron	N/A	ENSP00000232217.2
	RBP2	ENST00000511956.1	TSL:3	c.74-3147G>A		intron	N/A	ENSP00000424333.1
	COPB2-DT	ENST00000515247.5	TSL:4	n.317+42323C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.114 AC: 17346 AN: 151998 Hom.: 1992 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.0666

Gnomad ASJ AF: 0.0847

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.0978

Gnomad FIN AF: 0.0255

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0403

Gnomad OTH AF: 0.0994

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

GnomAD4 genome AF: 0.114 AC: 17377 AN: 152116 Hom.: 1998 Cov.: 32 AF XY: 0.112 AC XY: 8303 AN XY: 74358

African (AFR) AF: 0.293 AC: 12149 AN: 41434

American (AMR) AF: 0.0666 AC: 1018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0847 AC: 294 AN: 3472

East Asian (EAS) AF: 0.0294 AC: 152 AN: 5170

South Asian (SAS) AF: 0.0972 AC: 468 AN: 4814

European-Finnish (FIN) AF: 0.0255 AC: 271 AN: 10610

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0403 AC: 2739 AN: 68002

Other (OTH) AF: 0.102 AC: 216 AN: 2114

Alfa AF: 0.0644 Hom.: 358

Bravo AF: 0.124

Asia WGS AF: 0.0920 AC: 320 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.6
DANN	Benign	0.69
PhyloP100		0.49
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: rs16849083; hg19: chr3-139184279;