16-16142082-G-C

Position:

• chr16-16142082-G-C

Variant summary

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

The NM_004996.4(ABCC1):​c.*801G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.491 in 134,262 control chromosomes in the GnomAD database, including 14,829 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 0.49 (14829 hom., cov: 26)
  • Exomes 𝑓: 0.50 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: ABCC1 NM_004996.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.26

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCC1	NM_004996.4	c.*801G>C		3_prime_UTR_variant	31/31	ENST00000399410.8	NP_004987.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCC1	ENST00000399410.8	c.*801G>C		3_prime_UTR_variant	31/31	1	NM_004996.4	ENSP00000382342.3

Frequencies

GnomAD3 genomes AF: 0.491 AC: 65883 AN: 134144 Hom.: 14807 Cov.: 26

Gnomad AFR AF: 0.553

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.717

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.528

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.486

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 1.00

Gnomad4 NFE exome AF: 0.00

GnomAD4 genome AF: 0.491 AC: 65953 AN: 134262 Hom.: 14829 Cov.: 26 AF XY: 0.503 AC XY: 32575 AN XY: 64728

Gnomad4 AFR AF: 0.553

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.608

Gnomad4 FIN AF: 0.528

Gnomad4 NFE AF: 0.435

Gnomad4 OTH AF: 0.485

Alfa AF: 0.412 Hom.: 7490

Bravo AF: 0.446

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.65

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: rs129081; hg19: chr16-16235939;