Variant 16-16068162-T-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_004996.4(ABCC1):c.1684T>C(p.Leu562=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.817 in 1,613,856 control chromosomes in the GnomAD database, including 542,071 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 0.83 ( 52819 hom., cov: 31)

Exomes 𝑓: 0.82 ( 489252 hom. )

Consequence

ABCC1
NM_004996.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.480

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.67).

BP7

Synonymous conserved (PhyloP=0.48 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC1	NM_004996.4 linkuse as main transcript	c.1684T>C	p.Leu562=	synonymous_variant	13/31	ENST00000399410.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC1	ENST00000399410.8 linkuse as main transcript	c.1684T>C	p.Leu562=	synonymous_variant	13/31	1	NM_004996.4	P1	P33527-1

Frequencies

GnomAD3 genomes

AF:

0.832

AC:

126461

AN:

152052

Hom.:

52781

Cov.:

show subpopulations

Gnomad AFR

AF:

0.878

Gnomad AMI

AF:

0.931

Gnomad AMR

AF:

0.800

Gnomad ASJ

AF:

0.776

Gnomad EAS

AF:

0.796

Gnomad SAS

AF:

0.615

Gnomad FIN

AF:

0.838

Gnomad MID

AF:

0.737

Gnomad NFE

AF:

0.831

Gnomad OTH

AF:

0.805

GnomAD3 exomes

AF:

0.792

AC:

197671

AN:

249450

Hom.:

79152

AF XY:

0.784

AC XY:

106130

AN XY:

135330

show subpopulations

Gnomad AFR exome

AF:

0.879

Gnomad AMR exome

AF:

0.777

Gnomad ASJ exome

AF:

0.767

Gnomad EAS exome

AF:

0.791

Gnomad SAS exome

AF:

0.614

Gnomad FIN exome

AF:

0.839

Gnomad NFE exome

AF:

0.827

Gnomad OTH exome

AF:

0.797

GnomAD4 exome

AF:

0.816

AC:

1192679

AN:

1461686

Hom.:

489252

Cov.:

AF XY:

0.810

AC XY:

588637

AN XY:

727136

show subpopulations

Gnomad4 AFR exome

AF:

0.874

Gnomad4 AMR exome

AF:

0.781

Gnomad4 ASJ exome

AF:

0.767

Gnomad4 EAS exome

AF:

0.772

Gnomad4 SAS exome

AF:

0.616

Gnomad4 FIN exome

AF:

0.837

Gnomad4 NFE exome

AF:

0.834

Gnomad4 OTH exome

AF:

0.807

GnomAD4 genome

AF:

0.832

AC:

126547

AN:

152170

Hom.:

52819

Cov.:

AF XY:

0.826

AC XY:

61478

AN XY:

74398

show subpopulations

Gnomad4 AFR

AF:

0.878

Gnomad4 AMR

AF:

0.799

Gnomad4 ASJ

AF:

0.776

Gnomad4 EAS

AF:

0.796

Gnomad4 SAS

AF:

0.614

Gnomad4 FIN

AF:

0.838

Gnomad4 NFE

AF:

0.831

Gnomad4 OTH

AF:

0.799

Alfa

AF:

0.822

Hom.:

104427

Bravo

AF:

0.832

Asia WGS

AF:

0.718

AC:

2500

AN:

3478

EpiCase

AF:

0.821

EpiControl

AF:

0.809

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.67

CADD

Benign

3.8

DANN

Benign

0.35

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.7

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