Variant chr16-16134385-G-A 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.4002G>A(p.Ser1334=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.261 in 1,613,802 control chromosomes in the GnomAD database, including 57,722 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 0.22 ( 4412 hom., cov: 32)

Exomes 𝑓: 0.27 ( 53310 hom. )

Consequence

ABCC1
NM_004996.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.88

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=-0.85).

BP7

Synonymous conserved (PhyloP=-1.88 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.281 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.4002G>A	p.Ser1334=	synonymous_variant	28/31	ENST00000399410.8	NP_004987.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC1	ENST00000399410.8 linkuse as main transcript	c.4002G>A	p.Ser1334=	synonymous_variant	28/31	1	NM_004996.4	ENSP00000382342	P1	P33527-1

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34014

AN:

151846

Hom.:

4410

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0981

Gnomad AMI

AF:

0.340

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.224

Gnomad EAS

AF:

0.117

Gnomad SAS

AF:

0.169

Gnomad FIN

AF:

0.337

Gnomad MID

AF:

0.184

Gnomad NFE

AF:

0.280

Gnomad OTH

AF:

0.210

GnomAD3 exomes

AF:

0.249

AC:

62090

AN:

249422

Hom.:

8450

AF XY:

0.247

AC XY:

33396

AN XY:

135344

show subpopulations

Gnomad AFR exome

AF:

0.0934

Gnomad AMR exome

AF:

0.310

Gnomad ASJ exome

AF:

0.220

Gnomad EAS exome

AF:

0.115

Gnomad SAS exome

AF:

0.175

Gnomad FIN exome

AF:

0.332

Gnomad NFE exome

AF:

0.279

Gnomad OTH exome

AF:

0.254

GnomAD4 exome

AF:

0.265

AC:

387966

AN:

1461838

Hom.:

53310

Cov.:

AF XY:

0.263

AC XY:

190942

AN XY:

727220

show subpopulations

Gnomad4 AFR exome

AF:

0.0915

Gnomad4 AMR exome

AF:

0.310

Gnomad4 ASJ exome

AF:

0.218

Gnomad4 EAS exome

AF:

0.139

Gnomad4 SAS exome

AF:

0.176

Gnomad4 FIN exome

AF:

0.325

Gnomad4 NFE exome

AF:

0.280

Gnomad4 OTH exome

AF:

0.243

GnomAD4 genome

AF:

0.224

AC:

34022

AN:

151964

Hom.:

4412

Cov.:

AF XY:

0.225

AC XY:

16714

AN XY:

74258

show subpopulations

Gnomad4 AFR

AF:

0.0977

Gnomad4 AMR

AF:

0.288

Gnomad4 ASJ

AF:

0.224

Gnomad4 EAS

AF:

0.118

Gnomad4 SAS

AF:

0.169

Gnomad4 FIN

AF:

0.337

Gnomad4 NFE

AF:

0.280

Gnomad4 OTH

AF:

0.208

Alfa

AF:

0.265

Hom.:

8183

Bravo

AF:

0.213

Asia WGS

AF:

0.149

AC:

518

AN:

3478

EpiCase

AF:

0.267

EpiControl

AF:

0.264

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.43

DANN

Benign

0.66

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