3-139531807-A-G

Variant names:

• chr3-139531807-A-G
• rs893703
• NM_002899.5:c.438+6974T>C

Variant summary

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

The NM_002899.5(RBP1):​c.438+6974T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.153 in 152,168 control chromosomes in the GnomAD database, including 2,094 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 0.15 (2094 hom., cov: 32)
• Consequence: RBP1 NM_002899.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 8 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002899.5. 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
	RBP1	NM_002899.5	MANE Select	c.438+6974T>C		intron	N/A	NP_002890.2	A0A0A0MQT0
	RBP1	NM_001130992.3		c.439-4465T>C		intron	N/A	NP_001124464.1	P09455-3
	RBP1	NM_001130993.3		c.439-5905T>C		intron	N/A	NP_001124465.1	P09455-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RBP1	ENST00000672186.1	MANE Select	c.438+6974T>C		intron	N/A	ENSP00000500931.1	A0A0A0MQT0
	RBP1	ENST00000492918.1	TSL:1	c.439-4465T>C		intron	N/A	ENSP00000429166.1	P09455-3
	RBP1	ENST00000619087.5	TSL:1	c.252+6974T>C		intron	N/A	ENSP00000482165.1	P09455-1

Frequencies

GnomAD3 genomes AF: 0.153 AC: 23234 AN: 152050 Hom.: 2095 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.0639

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.156

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.153 AC: 23245 AN: 152168 Hom.: 2094 Cov.: 32 AF XY: 0.157 AC XY: 11714 AN XY: 74392

African (AFR) AF: 0.158 AC: 6558 AN: 41524

American (AMR) AF: 0.213 AC: 3252 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0639 AC: 222 AN: 3472

East Asian (EAS) AF: 0.451 AC: 2336 AN: 5174

South Asian (SAS) AF: 0.130 AC: 626 AN: 4822

European-Finnish (FIN) AF: 0.156 AC: 1653 AN: 10596

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.122 AC: 8278 AN: 67988

Other (OTH) AF: 0.129 AC: 271 AN: 2108

Alfa AF: 0.131 Hom.: 4642

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.52
PhyloP100		0.057
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: rs893703; hg19: chr3-139250649;