rs563694

Positions:

• chr2-168917561-C-A
• chr2-168917561-C-G

Variant summary

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

The ENST00000648875.1(ABCB11):​c.227-1879G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,158 control chromosomes in the GnomAD database, including 44,093 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 0.75 (44093 hom., cov: 32)
• Consequence: ABCB11 ENST00000648875.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

ABCB11 (HGNC:42): (ATP binding cassette subfamily B member 11) 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 the major canalicular bile salt export pump in man. Mutations in this gene cause a form of progressive familial intrahepatic cholestases which are a group of inherited disorders with severe cholestatic liver disease from early infancy. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCB11	XM_017005165.2	c.3868-1879G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCB11	ENST00000648875.1	c.227-1879G>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114489 AN: 152040 Hom.: 44034 Cov.: 32

Gnomad AFR AF: 0.891

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.778

Gnomad ASJ AF: 0.747

Gnomad EAS AF: 0.962

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.670

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.753 AC: 114608 AN: 152158 Hom.: 44093 Cov.: 32 AF XY: 0.757 AC XY: 56343 AN XY: 74382

Gnomad4 AFR AF: 0.892

Gnomad4 AMR AF: 0.779

Gnomad4 ASJ AF: 0.747

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.817

Gnomad4 FIN AF: 0.670

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.746

Alfa AF: 0.684 Hom.: 68683

Bravo AF: 0.769

Asia WGS AF: 0.863 AC: 2998 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	6.8
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs563694; hg19: chr2-169774071;