rs1186745

Variant names:

• chr7-87504631-C-A
• rs1186745
• NM_001348946.2:c.3637-182G>T

Variant summary

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

The NM_001348946.2(ABCB1):​c.3637-182G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,022 control chromosomes in the GnomAD database, including 1,386 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 0.13 (1386 hom., cov: 31)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.215
• Publications: 1 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001348946.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB1	NM_001348946.2	MANE Select	c.3637-182G>T		intron	N/A	NP_001335875.1
	ABCB1	NM_001348945.2		c.3847-182G>T		intron	N/A	NP_001335874.1
	ABCB1	NM_000927.5		c.3637-182G>T		intron	N/A	NP_000918.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCB1	ENST00000622132.5	TSL:1 MANE Select	c.3637-182G>T		intron	N/A	ENSP00000478255.1
	ABCB1	ENST00000265724.8	TSL:1	c.3637-182G>T		intron	N/A	ENSP00000265724.3
	ABCB1	ENST00000488737.6	TSL:1	n.1279-182G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19268 AN: 151902 Hom.: 1381 Cov.: 31

Gnomad AFR AF: 0.0588

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.180

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.127 AC: 19282 AN: 152022 Hom.: 1386 Cov.: 31 AF XY: 0.128 AC XY: 9545 AN XY: 74316

African (AFR) AF: 0.0586 AC: 2433 AN: 41484

American (AMR) AF: 0.191 AC: 2921 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.131 AC: 456 AN: 3468

East Asian (EAS) AF: 0.181 AC: 933 AN: 5150

South Asian (SAS) AF: 0.124 AC: 594 AN: 4808

European-Finnish (FIN) AF: 0.123 AC: 1299 AN: 10584

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.150 AC: 10183 AN: 67924

Other (OTH) AF: 0.142 AC: 300 AN: 2114

Alfa AF: 0.0763 Hom.: 176

Bravo AF: 0.128

Asia WGS AF: 0.138 AC: 482 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.34
DANN	Benign	0.38
PhyloP100		0.21
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: rs1186745; hg19: chr7-87133947;