3-139531807-A-G

Position:

• chr3-139531807-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RBP1	NM_002899.5	c.438+6974T>C		intron_variant		ENST00000672186.1	NP_002890.2
COPB2-DT	NR_121609.1	n.355-45985A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RBP1	ENST00000672186.1	c.438+6974T>C		intron_variant			NM_002899.5	ENSP00000500931
COPB2-DT	ENST00000658348.1	n.672-45985A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.158

Gnomad4 AMR AF: 0.213

Gnomad4 ASJ AF: 0.0639

Gnomad4 EAS AF: 0.451

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.156

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.129

Alfa AF: 0.126 Hom.: 2691

Bravo AF: 0.161

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	5.2
DANN	Benign	0.52

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: rs893703; hg19: chr3-139250649;