7-87540701-C-T

Variant names:

• chr7-87540701-C-T
• rs12154941
• NM_001348946.2:c.2319+656G>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.2319+656G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.333 in 152,080 control chromosomes in the GnomAD database, including 9,087 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 0.33 (9087 hom., cov: 32)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.673
• Publications: 2 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.397 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB1	NM_001348946.2	c.2319+656G>A		intron_variant	Intron 18 of 27	ENST00000622132.5	NP_001335875.1
ABCB1	NM_001348945.2	c.2529+656G>A		intron_variant	Intron 22 of 31		NP_001335874.1
ABCB1	NM_000927.5	c.2319+656G>A		intron_variant	Intron 19 of 28		NP_000918.2
ABCB1	NM_001348944.2	c.2319+656G>A		intron_variant	Intron 20 of 29		NP_001335873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB1	ENST00000622132.5	c.2319+656G>A		intron_variant	Intron 18 of 27	1	NM_001348946.2	ENSP00000478255.1
ABCB1	ENST00000265724.8	c.2319+656G>A		intron_variant	Intron 19 of 28	1		ENSP00000265724.3
ABCB1	ENST00000543898.5	c.2127+656G>A		intron_variant	Intron 18 of 27	5		ENSP00000444095.1

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50687 AN: 151964 Hom.: 9080 Cov.: 32

Gnomad AFR AF: 0.217

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.378

Gnomad ASJ AF: 0.437

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.395

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.401

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.333 AC: 50712 AN: 152080 Hom.: 9087 Cov.: 32 AF XY: 0.331 AC XY: 24612 AN XY: 74352

African (AFR) AF: 0.216 AC: 8980 AN: 41482

American (AMR) AF: 0.378 AC: 5775 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.437 AC: 1513 AN: 3466

East Asian (EAS) AF: 0.168 AC: 868 AN: 5176

South Asian (SAS) AF: 0.186 AC: 897 AN: 4812

European-Finnish (FIN) AF: 0.395 AC: 4182 AN: 10582

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.401 AC: 27268 AN: 67974

Other (OTH) AF: 0.370 AC: 781 AN: 2112

Alfa AF: 0.366 Hom.: 1176

Bravo AF: 0.327

Asia WGS AF: 0.184 AC: 647 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.82
DANN	Benign	0.77
PhyloP100		-0.67
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: rs12154941; hg19: chr7-87170017;