rs1893590

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000398457.6(ABCG1):​c.-464A>C variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 152,126 control chromosomes in the GnomAD database, including 10,139 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 0.35 ( 10139 hom., cov: 33)

Consequence

ABCG1
ENST00000398457.6 upstream_gene

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

22 publications found
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABCG1NM_207627.2 linkc.-464A>C upstream_gene_variant NP_997510.1 P45844-3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCG1ENST00000398457.6 linkc.-464A>C upstream_gene_variant 1 ENSP00000381475.2 P45844-3

Frequencies

GnomAD3 genomes
AF:
0.352
AC:
53582
AN:
152008
Hom.:
10128
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.475
Gnomad AMI
AF:
0.287
Gnomad AMR
AF:
0.362
Gnomad ASJ
AF:
0.366
Gnomad EAS
AF:
0.455
Gnomad SAS
AF:
0.357
Gnomad FIN
AF:
0.364
Gnomad MID
AF:
0.360
Gnomad NFE
AF:
0.267
Gnomad OTH
AF:
0.326
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.353
AC:
53643
AN:
152126
Hom.:
10139
Cov.:
33
AF XY:
0.357
AC XY:
26556
AN XY:
74356
show subpopulations
African (AFR)
AF:
0.476
AC:
19729
AN:
41488
American (AMR)
AF:
0.363
AC:
5547
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.366
AC:
1268
AN:
3468
East Asian (EAS)
AF:
0.455
AC:
2358
AN:
5178
South Asian (SAS)
AF:
0.356
AC:
1718
AN:
4828
European-Finnish (FIN)
AF:
0.364
AC:
3846
AN:
10564
Middle Eastern (MID)
AF:
0.370
AC:
108
AN:
292
European-Non Finnish (NFE)
AF:
0.267
AC:
18120
AN:
67992
Other (OTH)
AF:
0.325
AC:
688
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1755
3510
5265
7020
8775
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
508
1016
1524
2032
2540
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.297
Hom.:
13293
Bravo
AF:
0.357
Asia WGS
AF:
0.406
AC:
1415
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
1.2
DANN
Benign
0.57
PhyloP100
-0.031
PromoterAI
0.0022
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs1893590; hg19: chr21-43619595; API