7-87507702-C-T

Variant names:

• chr7-87507702-C-T
• rs1882478
• NM_001348946.2:c.3489+1573G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001348946.2(ABCB1):​c.3489+1573G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 151,702 control chromosomes in the GnomAD database, including 12,888 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 0.38 (12888 hom., cov: 31)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.94
• Publications: 9 publications found

Genes affected

ABCB1 (HGNC:40): (ATP binding cassette subfamily B member 1) The membrane-associated 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 protein is a member of the MDR/TAP subfamily. Members of the MDR/TAP subfamily are involved in multidrug resistance. The protein encoded by this gene is an ATP-dependent drug efflux pump for xenobiotic compounds with broad substrate specificity. It is responsible for decreased drug accumulation in multidrug-resistant cells and often mediates the development of resistance to anticancer drugs. This protein also functions as a transporter in the blood-brain barrier. Mutations in this gene are associated with colchicine resistance and Inflammatory bowel disease 13. Alternative splicing and the use of alternative promoters results in multiple transcript variants. [provided by RefSeq, Feb 2017]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.587 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB1	NM_001348946.2	c.3489+1573G>A		intron_variant	Intron 26 of 27	ENST00000622132.5	NP_001335875.1
ABCB1	NM_001348945.2	c.3699+1573G>A		intron_variant	Intron 30 of 31		NP_001335874.1
ABCB1	NM_000927.5	c.3489+1573G>A		intron_variant	Intron 27 of 28		NP_000918.2
ABCB1	NM_001348944.2	c.3489+1573G>A		intron_variant	Intron 28 of 29		NP_001335873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB1	ENST00000622132.5	c.3489+1573G>A		intron_variant	Intron 26 of 27	1	NM_001348946.2	ENSP00000478255.1

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58324 AN: 151584 Hom.: 12859 Cov.: 31

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.299

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.229

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.404

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.385 AC: 58395 AN: 151702 Hom.: 12888 Cov.: 31 AF XY: 0.383 AC XY: 28377 AN XY: 74114

African (AFR) AF: 0.594 AC: 24570 AN: 41386

American (AMR) AF: 0.407 AC: 6201 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.420 AC: 1456 AN: 3468

East Asian (EAS) AF: 0.573 AC: 2945 AN: 5144

South Asian (SAS) AF: 0.243 AC: 1170 AN: 4810

European-Finnish (FIN) AF: 0.229 AC: 2409 AN: 10510

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18436 AN: 67840

Other (OTH) AF: 0.402 AC: 845 AN: 2100

Alfa AF: 0.315 Hom.: 31538

Bravo AF: 0.411

Asia WGS AF: 0.400 AC: 1391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.12
DANN	Benign	0.61
PhyloP100		-2.9
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1882478; hg19: chr7-87137018;