Genetic Variant ABCG1:c.-17_-9dupGCCGCCGCC (chr21-42219222-C-CCCGCCGCCG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_016818.3(ABCG1):c.-17_-9dupGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,474,028 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00014 ( 0 hom., cov: 26)

Exomes 𝑓: 0.00011 ( 0 hom. )

Consequence

ABCG1
NM_016818.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0270

Publications

0 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]

ABCG1 links:

LOC105372814 (HGNC:):

LOC105372814 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016818.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCG1	NM_016818.3	MANE Select	c.-17_-9dupGCCGCCGCC	5_prime_UTR	Exon 1 of 15	NP_058198.2
ABCG1	NM_004915.4		c.-17_-9dupGCCGCCGCC	5_prime_UTR	Exon 1 of 15	NP_004906.3
ABCG1	NM_207627.2		c.49-6425_49-6417dupGCCGCCGCC	intron	N/A	NP_997510.1	P45844-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
ABCG1	ENST00000398449.8	TSL:1 MANE Select	c.-17_-9dupGCCGCCGCC	5_prime_UTR	Exon 1 of 15	ENSP00000381467.3	P45844-4
ABCG1	ENST00000361802.7	TSL:1	c.-17_-9dupGCCGCCGCC	5_prime_UTR	Exon 1 of 15	ENSP00000354995.2	P45844-1
ABCG1	ENST00000398457.6	TSL:1	c.49-6425_49-6417dupGCCGCCGCC	intron	N/A	ENSP00000381475.2	P45844-3

Frequencies

GnomAD3 genomes

AF:

0.000140

AC:

AN:

150178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000171

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000629

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000163

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000110

AC:

146

AN:

1323850

Hom.:

Cov.:

AF XY:

0.000112

AC XY:

AN XY:

653848

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.000221

AC:

AN:

27178

American (AMR)

AF:

0.00

AC:

AN:

30234

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

22844

East Asian (EAS)

AF:

0.00

AC:

AN:

30786

South Asian (SAS)

AF:

0.000133

AC:

AN:

75010

European-Finnish (FIN)

AF:

0.000176

AC:

AN:

34022

Middle Eastern (MID)

AF:

0.000571

AC:

AN:

5258

European-Non Finnish (NFE)

AF:

0.0000996

AC:

104

AN:

1043754

Other (OTH)

AF:

0.000310

AC:

AN:

54764

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.356

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.000140

AC:

AN:

150178

Hom.:

Cov.:

AF XY:

0.000136

AC XY:

AN XY:

73292

show subpopulations

African (AFR)

AF:

0.000171

AC:

AN:

40956

American (AMR)

AF:

0.00

AC:

AN:

15106

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3448

East Asian (EAS)

AF:

0.00

AC:

AN:

5096

South Asian (SAS)

AF:

0.000629

AC:

AN:

4770

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10188

Middle Eastern (MID)

AF:

0.00

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.000163

AC:

AN:

67344

Other (OTH)

AF:

0.00

AC:

AN:

2054

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.539

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00

Hom.:

167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.027

Splicing

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

21-42219222-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCGCCGCCGCCGCCG

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over