rs3789243

chr7-87591570-A-Gchr7-87591570-A-T

Variant summary

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

The NM_001348946.2(ABCB1):c.117+4196T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.503 in 151,786 control chromosomes in the GnomAD database, including 19,361 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 0.50 (19361 hom., cov: 31)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB1	NM_001348946.2	c.117+4196T>C		intron_variant		ENST00000622132.5
ABCB1	NM_000927.5	c.117+4196T>C		intron_variant
ABCB1	NM_001348944.2	c.117+4196T>C		intron_variant
ABCB1	NM_001348945.2	c.327+4196T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB1	ENST00000622132.5	c.117+4196T>C		intron_variant		1	NM_001348946.2	P1
ABCB1	ENST00000265724.8	c.117+4196T>C		intron_variant		1		P1
ABCB1	ENST00000416177.1	c.117+4196T>C		intron_variant		5
ABCB1	ENST00000543898.5	c.117+4196T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76369 AN: 151668 Hom.: 19355 Cov.: 31

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.507

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.424

Gnomad EAS AF: 0.615

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.501

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.503 AC: 76409 AN: 151786 Hom.: 19361 Cov.: 31 AF XY: 0.506 AC XY: 37554 AN XY: 74150

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.471

Gnomad4 ASJ AF: 0.424

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.676

Gnomad4 FIN AF: 0.529

Gnomad4 NFE AF: 0.501

Gnomad4 OTH AF: 0.481

Alfa AF: 0.503 Hom.: 38509

Bravo AF: 0.498

Asia WGS AF: 0.627 AC: 2179 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.3
Dann	Benign	0.21

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: rs3789243; hg19: chr7-87220886;