rs45607032

Positions:

• chr16-16090365-CAT-C

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_004996.4(ABCC1):​c.2461-39_2461-38del variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0173 in 1,536,314 control chromosomes in the GnomAD database, including 501 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.028 (91 hom., cov: 32)
  • Exomes 𝑓: 0.016 (410 hom.)
• Consequence: ABCC1 NM_004996.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

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 -8 ACMG points.

• BA1: GnomAdExome4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0758 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCC1	NM_004996.4	c.2461-39_2461-38del		intron_variant		ENST00000399410.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCC1	ENST00000399410.8	c.2461-39_2461-38del		intron_variant		1	NM_004996.4	P1

Frequencies

GnomAD3 genomes AF: 0.0280 AC: 4269 AN: 152214 Hom.: 90 Cov.: 32

Gnomad AFR AF: 0.0503

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0196

Gnomad EAS AF: 0.0509

Gnomad SAS AF: 0.0103

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0112

Gnomad OTH AF: 0.0258

GnomAD3 exomes AF: 0.0294 AC: 5607 AN: 190466 Hom.: 159 AF XY: 0.0259 AC XY: 2624 AN XY: 101144

Gnomad AFR exome AF: 0.0494

Gnomad AMR exome AF: 0.0834

Gnomad ASJ exome AF: 0.0219

Gnomad EAS exome AF: 0.0505

Gnomad SAS exome AF: 0.00669

Gnomad FIN exome AF: 0.0209

Gnomad NFE exome AF: 0.0131

Gnomad OTH exome AF: 0.0217

GnomAD4 exome AF: 0.0161 AC: 22294 AN: 1383982 Hom.: 410 AF XY: 0.0156 AC XY: 10560 AN XY: 678856

Gnomad4 AFR exome AF: 0.0512

Gnomad4 AMR exome AF: 0.0782

Gnomad4 ASJ exome AF: 0.0197

Gnomad4 EAS exome AF: 0.0622

Gnomad4 SAS exome AF: 0.00879

Gnomad4 FIN exome AF: 0.0197

Gnomad4 NFE exome AF: 0.0114

Gnomad4 OTH exome AF: 0.0181

GnomAD4 genome AF: 0.0281 AC: 4276 AN: 152332 Hom.: 91 Cov.: 32 AF XY: 0.0281 AC XY: 2094 AN XY: 74484

Gnomad4 AFR AF: 0.0502

Gnomad4 AMR AF: 0.0485

Gnomad4 ASJ AF: 0.0196

Gnomad4 EAS AF: 0.0510

Gnomad4 SAS AF: 0.0101

Gnomad4 FIN AF: 0.0229

Gnomad4 NFE AF: 0.0112

Gnomad4 OTH AF: 0.0269

Alfa AF: 0.0220 Hom.: 14

Bravo AF: 0.0324

Asia WGS AF: 0.0420 AC: 144 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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: rs45607032; hg19: chr16-16184222;