chr2-43845437-G-T

Variant names:

• chr2-43845437-G-T
• rs4299376
• NM_022437.3:c.166-718G>T

Variant summary

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

The NM_022437.3(ABCG8):​c.166-718G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.755 in 152,078 control chromosomes in the GnomAD database, including 43,918 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 0.76 (43918 hom., cov: 31)
• Consequence: ABCG8 NM_022437.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 159 publications found

Genes affected

ABCG8 (HGNC:13887): (ATP binding cassette subfamily G member 8) The 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 White subfamily. The protein encoded by this gene functions to exclude non-cholesterol sterol entry at the intestinal level, promote excretion of cholesterol and sterols into bile, and to facilitate transport of sterols back into the intestinal lumen. It is expressed in a tissue-specific manner in the liver, intestine, and gallbladder. This gene is tandemly arrayed on chromosome 2, in a head-to-head orientation with family member ABCG5. Mutations in this gene may contribute to sterol accumulation and atherosclerosis, and have been observed in patients with sitosterolemia. [provided by RefSeq, Jul 2008]

ABCG8 Gene-Disease associations (from GenCC):

• sitosterolemia

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Illumina
• sitosterolemia 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

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 (EAS) allele frequency at 95% confidence interval = 0.971 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ABCG8	NM_022437.3	c.166-718G>T		intron_variant	Intron 2 of 12	ENST00000272286.4	NP_071882.1
ABCG8	NM_001357321.2	c.166-718G>T		intron_variant	Intron 2 of 12		NP_001344250.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCG8	ENST00000272286.4	c.166-718G>T		intron_variant	Intron 2 of 12	1	NM_022437.3	ENSP00000272286.2
ABCG8	ENST00000644611.1	c.178-718G>T		intron_variant	Intron 2 of 8			ENSP00000495423.1
ABCG8	ENST00000643284.1	n.623-718G>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.755 AC: 114736 AN: 151960 Hom.: 43859 Cov.: 31

Gnomad AFR AF: 0.842

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.728

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.761

Gnomad FIN AF: 0.792

Gnomad MID AF: 0.646

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.755 AC: 114850 AN: 152078 Hom.: 43918 Cov.: 31 AF XY: 0.763 AC XY: 56715 AN XY: 74344

African (AFR) AF: 0.842 AC: 34929 AN: 41496

American (AMR) AF: 0.761 AC: 11625 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.728 AC: 2528 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5143 AN: 5174

South Asian (SAS) AF: 0.760 AC: 3655 AN: 4808

European-Finnish (FIN) AF: 0.792 AC: 8369 AN: 10562

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.681 AC: 46277 AN: 67976

Other (OTH) AF: 0.727 AC: 1535 AN: 2110

Alfa AF: 0.705 Hom.: 179784

Bravo AF: 0.760

Asia WGS AF: 0.885 AC: 3078 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	0.020
DANN	Benign	0.37
PhyloP100		-0.43
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: rs4299376; hg19: chr2-44072576;