rs8187710

Positions:

chr10-99851537-G-A

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000392.5(ABCC2):c.4544G>A(p.Cys1515Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0586 in 1,613,856 control chromosomes in the GnomAD database, including 3,546 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.083 ( 719 hom., cov: 33)

Exomes 𝑓: 0.056 ( 2827 hom. )

Consequence

ABCC2
NM_000392.5 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: 0.301

Variant links:

Genes affected

ABCC2 (HGNC:53): (ATP binding cassette subfamily C member 2) The protein encoded by this gene is a member of the superfamily of ATP-binding cassette (ABC) transporters. ABC proteins transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, White). This protein is a member of the MRP subfamily which is involved in multi-drug resistance. This protein is expressed in the canalicular (apical) part of the hepatocyte and functions in biliary transport. Substrates include anticancer drugs such as vinblastine; therefore, this protein appears to contribute to drug resistance in mammalian cells. Several different mutations in this gene have been observed in patients with Dubin-Johnson syndrome (DJS), an autosomal recessive disorder characterized by conjugated hyperbilirubinemia. [provided by RefSeq, Jul 2008]

ABCC2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0022177398).

BP6

Variant 10-99851537-G-A is Benign according to our data. Variant chr10-99851537-G-A is described in ClinVar as [Benign]. Clinvar id is 298481.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr10-99851537-G-A is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC2	NM_000392.5 linkuse as main transcript	c.4544G>A	p.Cys1515Tyr	missense_variant	32/32	ENST00000647814.1	NP_000383.2
ABCC2	XM_006717630.4 linkuse as main transcript	c.3848G>A	p.Cys1283Tyr	missense_variant	27/27		XP_006717693.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC2	ENST00000647814.1 linkuse as main transcript	c.4544G>A	p.Cys1515Tyr	missense_variant	32/32		NM_000392.5	ENSP00000497274	P1
ABCC2	ENST00000648523.1 linkuse as main transcript	c.*385G>A		3_prime_UTR_variant, NMD_transcript_variant	5/5			ENSP00000497778

Frequencies

GnomAD3 genomes

AF:

0.0825

AC:

12539

AN:

152076

Hom.:

709

Cov.:

show subpopulations

Gnomad AFR

AF:

0.158

Gnomad AMI

AF:

0.0329

Gnomad AMR

AF:

0.0704

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.000770

Gnomad SAS

AF:

0.0203

Gnomad FIN

AF:

0.0225

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.0572

Gnomad OTH

AF:

0.0903

GnomAD3 exomes

AF:

0.0528

AC:

13264

AN:

251416

Hom.:

576

AF XY:

0.0507

AC XY:

6891

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.157

Gnomad AMR exome

AF:

0.0414

Gnomad ASJ exome

AF:

0.129

Gnomad EAS exome

AF:

0.000707

Gnomad SAS exome

AF:

0.0184

Gnomad FIN exome

AF:

0.0225

Gnomad NFE exome

AF:

0.0572

Gnomad OTH exome

AF:

0.0658

GnomAD4 exome

AF:

0.0560

AC:

81918

AN:

1461662

Hom.:

2827

Cov.:

AF XY:

0.0549

AC XY:

39955

AN XY:

727138

show subpopulations

Gnomad4 AFR exome

AF:

0.163

Gnomad4 AMR exome

AF:

0.0451

Gnomad4 ASJ exome

AF:

0.132

Gnomad4 EAS exome

AF:

0.000302

Gnomad4 SAS exome

AF:

0.0188

Gnomad4 FIN exome

AF:

0.0233

Gnomad4 NFE exome

AF:

0.0569

Gnomad4 OTH exome

AF:

0.0673

GnomAD4 genome

AF:

0.0826

AC:

12578

AN:

152194

Hom.:

719

Cov.:

AF XY:

0.0793

AC XY:

5899

AN XY:

74428

show subpopulations

Gnomad4 AFR

AF:

0.158

Gnomad4 AMR

AF:

0.0703

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.000771

Gnomad4 SAS

AF:

0.0207

Gnomad4 FIN

AF:

0.0225

Gnomad4 NFE

AF:

0.0572

Gnomad4 OTH

AF:

0.0899

Alfa

AF:

0.0644

Hom.:

1024

Bravo

AF:

0.0916

TwinsUK

AF:

0.0615

AC:

228

ALSPAC

AF:

0.0558

AC:

215

ESP6500AA

AF:

0.157

AC:

692

ESP6500EA

AF:

0.0620

AC:

533

ExAC

AF:

0.0524

AC:

6359

Asia WGS

AF:

0.0270

AC:

AN:

3478

EpiCase

AF:

0.0665

EpiControl

AF:

0.0734

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:3

Benign, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Feb 01, 2024	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Nov 10, 2018	This variant is associated with the following publications: (PMID: 25087612, 18926681, 22027652) -
Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -

ABCC2-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Mar 06, 2024

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Dubin-Johnson syndrome

Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Mar 06, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.043

BayesDel_addAF

Benign

-0.69

BayesDel_noAF

Benign

-0.62

CADD

Benign

2.3

DANN

Benign

0.58

DEOGEN2

Benign

0.062

T;T

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.88

FATHMM_MKL

Benign

0.045

LIST_S2

Benign

0.67

.;T

MetaRNN

Benign

0.0022

T;T

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-0.48

N;N

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.52

PROVEAN

Benign

4.1

.;N

REVEL

Benign

0.11

Sift

Benign

0.63

.;T

Sift4G

Benign

0.25

.;T

Polyphen

0.0

B;B

Vest4

0.018

MPC

0.052

ClinPred

0.0051

GERP RS

2.0

Varity_R

0.084

gMVP

0.41

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