7-87589031-A-G

Variant names:

• chr7-87589031-A-G
• rs7802773
• NM_001348946.2:c.118-3351T>C

Variant summary

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

The NM_001348946.2(ABCB1):​c.118-3351T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 151,948 control chromosomes in the GnomAD database, including 20,214 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 0.51 (20214 hom., cov: 32)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.584
• Publications: 10 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=-0.98).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB1	NM_001348946.2	c.118-3351T>C		intron_variant	Intron 3 of 27	ENST00000622132.5	NP_001335875.1
ABCB1	NM_001348945.2	c.328-3351T>C		intron_variant	Intron 7 of 31		NP_001335874.1
ABCB1	NM_000927.5	c.118-3351T>C		intron_variant	Intron 4 of 28		NP_000918.2
ABCB1	NM_001348944.2	c.118-3351T>C		intron_variant	Intron 5 of 29		NP_001335873.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB1	ENST00000622132.5	c.118-3351T>C		intron_variant	Intron 3 of 27	1	NM_001348946.2	ENSP00000478255.1
ABCB1	ENST00000265724.8	c.118-3351T>C		intron_variant	Intron 4 of 28	1		ENSP00000265724.3
ABCB1	ENST00000543898.5	c.118-3351T>C		intron_variant	Intron 4 of 27	5		ENSP00000444095.1
ABCB1	ENST00000416177.1	c.118-3351T>C		intron_variant	Intron 5 of 5	5		ENSP00000399419.1

Frequencies

GnomAD3 genomes AF: 0.515 AC: 78144 AN: 151828 Hom.: 20198 Cov.: 32

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.616

Gnomad SAS AF: 0.678

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.515 AC: 78197 AN: 151948 Hom.: 20214 Cov.: 32 AF XY: 0.517 AC XY: 38429 AN XY: 74284

African (AFR) AF: 0.507 AC: 20993 AN: 41416

American (AMR) AF: 0.481 AC: 7343 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1531 AN: 3466

East Asian (EAS) AF: 0.615 AC: 3175 AN: 5160

South Asian (SAS) AF: 0.675 AC: 3251 AN: 4814

European-Finnish (FIN) AF: 0.534 AC: 5629 AN: 10548

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34622 AN: 67962

Other (OTH) AF: 0.488 AC: 1030 AN: 2110

Alfa AF: 0.508 Hom.: 2725

Bravo AF: 0.510

Asia WGS AF: 0.630 AC: 2183 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.78
DANN	Benign	0.38
PhyloP100		-0.58
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: rs7802773; hg19: chr7-87218347;