NM_016818.3:c.-26_-9dupGCCGCCGCCGCCGCCGCC

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_016818.3(ABCG1):​c.-26_-9dupGCCGCCGCCGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00256 in 150,280 control chromosomes in the GnomAD database, including 4 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0026 ( 4 hom., cov: 26)
Exomes 𝑓: 0.000082 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

ABCG1
NM_016818.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -4 ACMG points.

BS2
High Homozygotes in GnomAd4 at 4 AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ABCG1NM_016818.3 linkc.-26_-9dupGCCGCCGCCGCCGCCGCC 5_prime_UTR_variant Exon 1 of 15 ENST00000398449.8 NP_058198.2 P45844-4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ABCG1ENST00000398449 linkc.-26_-9dupGCCGCCGCCGCCGCCGCC 5_prime_UTR_variant Exon 1 of 15 1 NM_016818.3 ENSP00000381467.3 P45844-4

Frequencies

GnomAD3 genomes
AF:
0.00255
AC:
383
AN:
150176
Hom.:
4
Cov.:
26
show subpopulations
Gnomad AFR
AF:
0.00913
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000397
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000148
Gnomad OTH
AF:
0.000974
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
0.0000816
AC:
108
AN:
1323804
Hom.:
0
Cov.:
20
AF XY:
0.0000826
AC XY:
54
AN XY:
653828
show subpopulations
Gnomad4 AFR exome
AF:
0.00358
Gnomad4 AMR exome
AF:
0.0000331
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000192
Gnomad4 OTH exome
AF:
0.000146
GnomAD4 genome
AF:
0.00256
AC:
384
AN:
150280
Hom.:
4
Cov.:
26
AF XY:
0.00238
AC XY:
175
AN XY:
73402
show subpopulations
Gnomad4 AFR
AF:
0.00913
Gnomad4 AMR
AF:
0.000397
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000149
Gnomad4 OTH
AF:
0.000962

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2234716; hg19: chr21-43639332; API