Variant rs212088 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_004996.4(ABCC1):c.4487+18G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 1,549,228 control chromosomes in the GnomAD database, including 24,529 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 0.16 ( 1901 hom., cov: 31)

Exomes 𝑓: 0.18 ( 22628 hom. )

Consequence

ABCC1
NM_004996.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.147

Variant links:

Genes affected

ABCC1 (HGNC:51): (ATP binding cassette subfamily C member 1 (ABCC1 blood group)) 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 full transporter is a member of the MRP subfamily which is involved in multi-drug resistance. This protein functions as a multispecific organic anion transporter, with oxidized glutatione, cysteinyl leukotrienes, and activated aflatoxin B1 as substrates. This protein also transports glucuronides and sulfate conjugates of steroid hormones and bile salts. Alternatively spliced variants of this gene have been described but their full-length nature is unknown. [provided by RefSeq, Apr 2012]

ABCC1 links:

ABCC1 (HGNC:):

ABCC1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.233 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC1	NM_004996.4 linkuse as main transcript	c.4487+18G>A		intron_variant		ENST00000399410.8	NP_004987.2	P33527-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC1	ENST00000399410.8 linkuse as main transcript	c.4487+18G>A		intron_variant		1	NM_004996.4	ENSP00000382342.3		P33527-1

Frequencies

GnomAD3 genomes

AF:

0.156

AC:

23703

AN:

152038

Hom.:

1901

Cov.:

show subpopulations

Gnomad AFR

AF:

0.133

Gnomad AMI

AF:

0.119

Gnomad AMR

AF:

0.153

Gnomad ASJ

AF:

0.122

Gnomad EAS

AF:

0.244

Gnomad SAS

AF:

0.108

Gnomad FIN

AF:

0.116

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.176

Gnomad OTH

AF:

0.167

GnomAD3 exomes

AF:

0.160

AC:

34010

AN:

212392

Hom.:

2822

AF XY:

0.162

AC XY:

18601

AN XY:

115038

show subpopulations

Gnomad AFR exome

AF:

0.132

Gnomad AMR exome

AF:

0.115

Gnomad ASJ exome

AF:

0.125

Gnomad EAS exome

AF:

0.247

Gnomad SAS exome

AF:

0.116

Gnomad FIN exome

AF:

0.122

Gnomad NFE exome

AF:

0.183

Gnomad OTH exome

AF:

0.175

GnomAD4 exome

AF:

0.176

AC:

246555

AN:

1397072

Hom.:

22628

Cov.:

AF XY:

0.175

AC XY:

120103

AN XY:

686858

show subpopulations

Gnomad4 AFR exome

AF:

0.130

Gnomad4 AMR exome

AF:

0.115

Gnomad4 ASJ exome

AF:

0.118

Gnomad4 EAS exome

AF:

0.259

Gnomad4 SAS exome

AF:

0.112

Gnomad4 FIN exome

AF:

0.121

Gnomad4 NFE exome

AF:

0.186

Gnomad4 OTH exome

AF:

0.168

GnomAD4 genome

AF:

0.156

AC:

23702

AN:

152156

Hom.:

1901

Cov.:

AF XY:

0.154

AC XY:

11482

AN XY:

74400

show subpopulations

Gnomad4 AFR

AF:

0.133

Gnomad4 AMR

AF:

0.153

Gnomad4 ASJ

AF:

0.122

Gnomad4 EAS

AF:

0.244

Gnomad4 SAS

AF:

0.107

Gnomad4 FIN

AF:

0.116

Gnomad4 NFE

AF:

0.176

Gnomad4 OTH

AF:

0.167

Alfa

AF:

0.148

Hom.:

357

Bravo

AF:

0.159

Asia WGS

AF:

0.154

AC:

538

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.54

DANN

Benign

0.35

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over