Variant rs17265551 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.1677+56C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0831 in 1,579,524 control chromosomes in the GnomAD database, including 5,820 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 0.074 ( 457 hom., cov: 32)

Exomes 𝑓: 0.084 ( 5363 hom. )

Consequence

ABCC1
NM_004996.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.247

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:

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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=-0.87).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0876 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC1	NM_004996.4 link	c.1677+56C>T		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 link	c.1677+56C>T		intron_variant		1	NM_004996.4	ENSP00000382342.3		P33527-1

Frequencies

GnomAD3 genomes

AF:

0.0743

AC:

11293

AN:

152042

Hom.:

456

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0640

Gnomad AMI

AF:

0.00877

Gnomad AMR

AF:

0.0658

Gnomad ASJ

AF:

0.126

Gnomad EAS

AF:

0.0379

Gnomad SAS

AF:

0.0630

Gnomad FIN

AF:

0.0337

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.0895

Gnomad OTH

AF:

0.0991

GnomAD3 exomes

AF:

0.0727

AC:

16635

AN:

228728

Hom.:

623

AF XY:

0.0749

AC XY:

9333

AN XY:

124680

show subpopulations

Gnomad AFR exome

AF:

0.0652

Gnomad AMR exome

AF:

0.0448

Gnomad ASJ exome

AF:

0.123

Gnomad EAS exome

AF:

0.0349

Gnomad SAS exome

AF:

0.0644

Gnomad FIN exome

AF:

0.0362

Gnomad NFE exome

AF:

0.0929

Gnomad OTH exome

AF:

0.0907

GnomAD4 exome

AF:

0.0840

AC:

119894

AN:

1427364

Hom.:

5363

Cov.:

AF XY:

0.0841

AC XY:

59779

AN XY:

710566

show subpopulations

Gnomad4 AFR exome

AF:

0.0642

Gnomad4 AMR exome

AF:

0.0476

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.0416

Gnomad4 SAS exome

AF:

0.0642

Gnomad4 FIN exome

AF:

0.0388

Gnomad4 NFE exome

AF:

0.0901

Gnomad4 OTH exome

AF:

0.0865

GnomAD4 genome

AF:

0.0742

AC:

11292

AN:

152160

Hom.:

457

Cov.:

AF XY:

0.0717

AC XY:

5333

AN XY:

74394

show subpopulations

Gnomad4 AFR

AF:

0.0639

Gnomad4 AMR

AF:

0.0656

Gnomad4 ASJ

AF:

0.126

Gnomad4 EAS

AF:

0.0379

Gnomad4 SAS

AF:

0.0627

Gnomad4 FIN

AF:

0.0337

Gnomad4 NFE

AF:

0.0895

Gnomad4 OTH

AF:

0.0976

Alfa

AF:

0.0894

Hom.:

636

Bravo

AF:

0.0754

Asia WGS

AF:

0.0550

AC:

194

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.4

DANN

Benign

0.48

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.0

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