rs2097937

Variant names:

• chr7-87401587-G-A
• rs2097937
• XR_007060045.1:n.4237+246C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-87401587-G-A
• chr7-87401587-G-C

Variant summary

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

The XR_007060045.1(ABCB4):​n.4237+246C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 207,796 control chromosomes in the GnomAD database, including 57,797 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 0.71 (40063 hom., cov: 32)
  • Exomes 𝑓: 0.80 (17734 hom.)
• Consequence: ABCB4 XR_007060045.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

ABCB4 (HGNC:45): (ATP binding cassette subfamily B member 4) 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 as well as antigen presentation. This gene encodes a full transporter and member of the p-glycoprotein family of membrane proteins with phosphatidylcholine as its substrate. The function of this protein has not yet been determined; however, it may involve transport of phospholipids from liver hepatocytes into bile. Alternative splicing of this gene results in several products of undetermined function. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCB4	NM_000443.4	c.*509C>T		downstream_gene_variant		ENST00000649586.2	NP_000434.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCB4	ENST00000649586.2	c.*509C>T		downstream_gene_variant			NM_000443.4	ENSP00000496956.2
ABCB4	ENST00000440025.1	c.*335C>T		downstream_gene_variant		3		ENSP00000395716.1

Frequencies

GnomAD3 genomes AF: 0.711 AC: 108024 AN: 151922 Hom.: 40067 Cov.: 32

Gnomad AFR AF: 0.476

Gnomad AMI AF: 0.860

Gnomad AMR AF: 0.783

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.700

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.756

GnomAD4 exome AF: 0.795 AC: 44329 AN: 55754 Hom.: 17734 AF XY: 0.793 AC XY: 23367 AN XY: 29464

Gnomad4 AFR exome AF: 0.494

Gnomad4 AMR exome AF: 0.723

Gnomad4 ASJ exome AF: 0.847

Gnomad4 EAS exome AF: 0.708

Gnomad4 SAS exome AF: 0.752

Gnomad4 FIN exome AF: 0.808

Gnomad4 NFE exome AF: 0.828

Gnomad4 OTH exome AF: 0.784

GnomAD4 genome AF: 0.711 AC: 108048 AN: 152042 Hom.: 40063 Cov.: 32 AF XY: 0.712 AC XY: 52911 AN XY: 74330

Gnomad4 AFR AF: 0.476

Gnomad4 AMR AF: 0.783

Gnomad4 ASJ AF: 0.807

Gnomad4 EAS AF: 0.701

Gnomad4 SAS AF: 0.728

Gnomad4 FIN AF: 0.792

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.751

Alfa AF: 0.793 Hom.: 67944

Bravo AF: 0.699

Asia WGS AF: 0.707 AC: 2453 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.84
DANN	Benign	0.41

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2097937; hg19: chr7-87030903;