rs15661

Variant names:

• chr21-42304243-G-A
• rs15661
• ENST00000361802.7:c.*7851G>A

Variant summary

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

The ENST00000361802.7(ABCG1):​c.*7851G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.618 in 152,000 control chromosomes in the GnomAD database, including 29,090 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 0.62 (29090 hom., cov: 32)
• Consequence: ABCG1 ENST00000361802.7 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.560
• Publications: 4 publications found

Genes affected

ABCG1 (HGNC:73): (ATP binding cassette subfamily G member 1) 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. It is involved in macrophage cholesterol and phospholipids transport, and may regulate cellular lipid homeostasis in other cell types. Six alternative splice variants have been identified. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.615 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ABCG1	ENST00000361802.7	c.*7851G>A		3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000354995.2

Frequencies

GnomAD3 genomes AF: 0.618 AC: 93861 AN: 151882 Hom.: 29072 Cov.: 32

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.519

Gnomad SAS AF: 0.569

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.620

Gnomad OTH AF: 0.615

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

GnomAD4 genome AF: 0.618 AC: 93931 AN: 152000 Hom.: 29090 Cov.: 32 AF XY: 0.620 AC XY: 46060 AN XY: 74302

African (AFR) AF: 0.619 AC: 25636 AN: 41412

American (AMR) AF: 0.596 AC: 9100 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2392 AN: 3466

East Asian (EAS) AF: 0.519 AC: 2684 AN: 5176

South Asian (SAS) AF: 0.570 AC: 2740 AN: 4810

European-Finnish (FIN) AF: 0.680 AC: 7199 AN: 10582

Middle Eastern (MID) AF: 0.612 AC: 180 AN: 294

European-Non Finnish (NFE) AF: 0.620 AC: 42157 AN: 67968

Other (OTH) AF: 0.614 AC: 1295 AN: 2110

Alfa AF: 0.616 Hom.: 55062

Bravo AF: 0.612

Asia WGS AF: 0.547 AC: 1906 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.0
DANN	Benign	0.73
PhyloP100		0.56

Splicing

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

Other links and lift over

dbSNP: rs15661; hg19: chr21-43724353;