7-87542343-T-C

Position:

• chr7-87542343-T-C

Variant summary

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

The NM_001348946.2(ABCB1):​c.2212-879A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.576 in 152,046 control chromosomes in the GnomAD database, including 25,772 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 0.58 (25772 hom., cov: 33)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
ABCB1	NM_001348946.2	c.2212-879A>G		intron_variant		ENST00000622132.5	NP_001335875.1
ABCB1	NM_000927.5	c.2212-879A>G		intron_variant			NP_000918.2
ABCB1	NM_001348944.2	c.2212-879A>G		intron_variant			NP_001335873.1
ABCB1	NM_001348945.2	c.2422-879A>G		intron_variant			NP_001335874.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ABCB1	ENST00000622132.5	c.2212-879A>G		intron_variant		1	NM_001348946.2	ENSP00000478255	P1
ABCB1	ENST00000265724.8	c.2212-879A>G		intron_variant		1		ENSP00000265724	P1
ABCB1	ENST00000543898.5	c.2020-879A>G		intron_variant		5		ENSP00000444095

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87433 AN: 151928 Hom.: 25720 Cov.: 33

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.554

Gnomad ASJ AF: 0.622

Gnomad EAS AF: 0.367

Gnomad SAS AF: 0.387

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.550

Gnomad OTH AF: 0.595

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

GnomAD4 genome AF: 0.576 AC: 87557 AN: 152046 Hom.: 25772 Cov.: 33 AF XY: 0.569 AC XY: 42279 AN XY: 74306

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.555

Gnomad4 ASJ AF: 0.622

Gnomad4 EAS AF: 0.367

Gnomad4 SAS AF: 0.388

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.550

Gnomad4 OTH AF: 0.593

Alfa AF: 0.357 Hom.: 726

Bravo AF: 0.587

Asia WGS AF: 0.414 AC: 1446 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.64

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: rs4728700; hg19: chr7-87171659;