rs2373589

chr7-87522342-C-T

Variant summary

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

The NM_001348946.2(ABCB1):c.2686-1466G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.204 in 735,994 control chromosomes in the GnomAD database, including 17,860 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 0.23 (4541 hom., cov: 32)
  • Exomes 𝑓: 0.20 (13319 hom.)
• Consequence: ABCB1 NM_001348946.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.54

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]

HNRNPA1P9 (HGNC:39127): (heterogeneous nuclear ribonucleoprotein A1 pseudogene 9)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.439 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB1	NM_001348946.2	c.2686-1466G>A		intron_variant		ENST00000622132.5
ABCB1	NM_000927.5	c.2686-1466G>A		intron_variant
ABCB1	NM_001348944.2	c.2686-1466G>A		intron_variant
ABCB1	NM_001348945.2	c.2896-1466G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB1	ENST00000622132.5	c.2686-1466G>A		intron_variant		1	NM_001348946.2	P1
HNRNPA1P9	ENST00000450624.1	n.882C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34315 AN: 151964 Hom.: 4524 Cov.: 32

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.456

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.111

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.221

GnomAD4 exome AF: 0.198 AC: 115505 AN: 583912 Hom.: 13319 Cov.: 4 AF XY: 0.195 AC XY: 62609 AN XY: 320584

Gnomad4 AFR exome AF: 0.346

Gnomad4 AMR exome AF: 0.251

Gnomad4 ASJ exome AF: 0.210

Gnomad4 EAS exome AF: 0.453

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.125

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.206

GnomAD4 genome AF: 0.226 AC: 34371 AN: 152082 Hom.: 4541 Cov.: 32 AF XY: 0.225 AC XY: 16737 AN XY: 74330

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.203

Gnomad4 EAS AF: 0.454

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.111

Gnomad4 NFE AF: 0.163

Gnomad4 OTH AF: 0.224

Alfa AF: 0.206 Hom.: 548

Bravo AF: 0.242

Asia WGS AF: 0.327 AC: 1135 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	1.8
Dann	Benign	0.49

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: rs2373589; hg19: chr7-87151658;