Variant 3-139538761-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_002899.5(RBP1):c.438+20T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 1,613,698 control chromosomes in the GnomAD database, including 38,513 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.27 ( 6568 hom., cov: 33)

Exomes 𝑓: 0.20 ( 31945 hom. )

Consequence

RBP1
NM_002899.5 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.973

Variant links:

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]

RBP1 links:

COPB2-DT (HGNC:55579): (COPB2 divergent transcript)

COPB2-DT links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BP6

Variant 3-139538761-A-G is Benign according to our data. Variant chr3-139538761-A-G is described in ClinVar as [Benign]. Clinvar id is 1586963.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.432 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RBP1	NM_002899.5 linkuse as main transcript	c.438+20T>C		intron_variant		ENST00000672186.1
COPB2-DT	NR_121609.1 linkuse as main transcript	n.355-39031A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RBP1	ENST00000672186.1 linkuse as main transcript	c.438+20T>C		intron_variant			NM_002899.5
COPB2-DT	ENST00000658348.1 linkuse as main transcript	n.672-39031A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.269

AC:

40955

AN:

152004

Hom.:

6537

Cov.:

show subpopulations

Gnomad AFR

AF:

0.437

Gnomad AMI

AF:

0.0987

Gnomad AMR

AF:

0.360

Gnomad ASJ

AF:

0.127

Gnomad EAS

AF:

0.218

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.193

Gnomad MID

AF:

0.190

Gnomad NFE

AF:

0.181

Gnomad OTH

AF:

0.222

GnomAD3 exomes

AF:

0.242

AC:

60707

AN:

251334

Hom.:

9308

AF XY:

0.223

AC XY:

30288

AN XY:

135856

show subpopulations

Gnomad AFR exome

AF:

0.441

Gnomad AMR exome

AF:

0.484

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.230

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.189

Gnomad NFE exome

AF:

0.181

Gnomad OTH exome

AF:

0.211

GnomAD4 exome

AF:

0.197

AC:

288459

AN:

1461576

Hom.:

31945

Cov.:

AF XY:

0.193

AC XY:

140650

AN XY:

727118

show subpopulations

Gnomad4 AFR exome

AF:

0.443

Gnomad4 AMR exome

AF:

0.467

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.173

Gnomad4 FIN exome

AF:

0.194

Gnomad4 NFE exome

AF:

0.182

Gnomad4 OTH exome

AF:

0.200

GnomAD4 genome

AF:

0.270

AC:

41053

AN:

152122

Hom.:

6568

Cov.:

AF XY:

0.271

AC XY:

20171

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.437

Gnomad4 AMR

AF:

0.361

Gnomad4 ASJ

AF:

0.127

Gnomad4 EAS

AF:

0.218

Gnomad4 SAS

AF:

0.176

Gnomad4 FIN

AF:

0.193

Gnomad4 NFE

AF:

0.181

Gnomad4 OTH

AF:

0.221

Alfa

AF:

0.201

Hom.:

4967

Bravo

AF:

0.295

Asia WGS

AF:

0.209

AC:

727

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

1.4

DANN

Benign

0.83

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over