rs3887893

chr16-16111644-T-Cchr16-16111644-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_004996.4(ABCC1):c.3079+62T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.409 in 1,468,488 control chromosomes in the GnomAD database, including 124,566 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 0.40 (12065 hom., cov: 32)
  • Exomes 𝑓: 0.41 (112501 hom.)
• Consequence: ABCC1 NM_004996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.01

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.537 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC1	NM_004996.4	c.3079+62T>C		intron_variant		ENST00000399410.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC1	ENST00000399410.8	c.3079+62T>C		intron_variant		1	NM_004996.4	P1

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60359 AN: 151848 Hom.: 12045 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.335

Gnomad ASJ AF: 0.425

Gnomad EAS AF: 0.547

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.387

GnomAD4 exome AF: 0.410 AC: 540182 AN: 1316522 Hom.: 112501 AF XY: 0.415 AC XY: 271297 AN XY: 653908

Gnomad4 AFR exome AF: 0.386

Gnomad4 AMR exome AF: 0.335

Gnomad4 ASJ exome AF: 0.451

Gnomad4 EAS exome AF: 0.534

Gnomad4 SAS exome AF: 0.555

Gnomad4 FIN exome AF: 0.393

Gnomad4 NFE exome AF: 0.397

Gnomad4 OTH exome AF: 0.426

GnomAD4 genome AF: 0.398 AC: 60421 AN: 151966 Hom.: 12065 Cov.: 32 AF XY: 0.401 AC XY: 29753 AN XY: 74288

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.425

Gnomad4 EAS AF: 0.547

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.404

Gnomad4 OTH AF: 0.392

Alfa AF: 0.409 Hom.: 17056

Bravo AF: 0.391

Asia WGS AF: 0.492 AC: 1709 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	0.013
Dann	Benign	0.44

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

Other links and lift over

dbSNP: rs3887893; hg19: chr16-16205501;