Genetic Variant ABCG1:c.-17_-9delGCCGCCGCC (chr21-42219222-CCCGCCGCCG-C) – 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_-9delGCCGCCGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000376 in 1,470,270 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00045 ( 0 hom., cov: 26)

Exomes 𝑓: 0.00037 ( 1 hom. )

Consequence

ABCG1
NM_016818.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.20

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:

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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_-9delGCCGCCGCC	5_prime_UTR	Exon 1 of 15	NP_058198.2
ABCG1	NM_004915.4		c.-17_-9delGCCGCCGCC	5_prime_UTR	Exon 1 of 15	NP_004906.3
ABCG1	NM_207627.2		c.49-6425_49-6417delGCCGCCGCC	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_-9delGCCGCCGCC	5_prime_UTR	Exon 1 of 15	ENSP00000381467.3	P45844-4
ABCG1	ENST00000361802.7	TSL:1	c.-17_-9delGCCGCCGCC	5_prime_UTR	Exon 1 of 15	ENSP00000354995.2	P45844-1
ABCG1	ENST00000398457.6	TSL:1	c.49-6425_49-6417delGCCGCCGCC	intron	N/A	ENSP00000381475.2	P45844-3

Frequencies

GnomAD3 genomes

AF:

0.000439

AC:

AN:

150178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000317

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00172

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000210

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000386

Gnomad OTH

AF:

0.00

GnomAD2 exomes

AF:

0.000932

AC:

AN:

76150

AF XY:

0.000820

show subpopulations

Gnomad AFR exome

AF:

0.00201

Gnomad AMR exome

AF:

0.00168

Gnomad ASJ exome

AF:

0.000410

Gnomad EAS exome

AF:

0.00118

Gnomad FIN exome

AF:

0.000404

Gnomad NFE exome

AF:

0.000729

Gnomad OTH exome

AF:

0.00146

GnomAD4 exome

AF:

0.000368

AC:

486

AN:

1319988

Hom.:

AF XY:

0.000385

AC XY:

251

AN XY:

651838

show subpopulations

African (AFR)

AF:

0.000700

AC:

AN:

27150

American (AMR)

AF:

0.00110

AC:

AN:

30056

Ashkenazi Jewish (ASJ)

AF:

0.000352

AC:

AN:

22726

East Asian (EAS)

AF:

0.000784

AC:

AN:

30604

South Asian (SAS)

AF:

0.000683

AC:

AN:

74644

European-Finnish (FIN)

AF:

0.000327

AC:

AN:

33682

Middle Eastern (MID)

AF:

0.00114

AC:

AN:

5246

European-Non Finnish (NFE)

AF:

0.000308

AC:

321

AN:

1041328

Other (OTH)

AF:

0.000238

AC:

AN:

54552

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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:

0.000446

AC:

AN:

150282

Hom.:

Cov.:

AF XY:

0.000436

AC XY:

AN XY:

73404

show subpopulations

African (AFR)

AF:

0.000341

AC:

AN:

41070

American (AMR)

AF:

0.00172

AC:

AN:

15126

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3448

East Asian (EAS)

AF:

0.00

AC:

AN:

5080

South Asian (SAS)

AF:

0.000210

AC:

AN:

4764

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10188

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.000386

AC:

AN:

67334

Other (OTH)

AF:

0.00

AC:

AN:

2078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

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:

0.00103

Hom.:

167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Mutation Taster

=270/30

polymorphism

(source)

Splicing

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

Publications

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21-42219222-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCG

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