Genetic Variant ABCG1:c.-11_-9dupGCC (chr21-42219222-C-CCCG) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP6BS2

The NM_016818.3(ABCG1):c.-11_-9dupGCC variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00166 in 1,472,956 control chromosomes in the GnomAD database, including 8 homozygotes. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.0045 ( 5 hom., cov: 26)

Exomes 𝑓: 0.0013 ( 3 hom. )

Consequence

ABCG1
NM_016818.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

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:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -5 ACMG points.

BP6

Variant 21-42219222-C-CCCG is Benign according to our data. Variant chr21-42219222-C-CCCG is described in ClinVar as Benign. ClinVar VariationId is 3041521.Status of the report is no_assertion_criteria_provided, 0 stars.

BS2

High Homozygotes in GnomAd4 at 5 AR gene

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.-11_-9dupGCC	5_prime_UTR	Exon 1 of 15	NP_058198.2
ABCG1	NM_004915.4		c.-11_-9dupGCC	5_prime_UTR	Exon 1 of 15	NP_004906.3
ABCG1	NM_207627.2		c.49-6419_49-6417dupGCC	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.-11_-9dupGCC	5_prime_UTR	Exon 1 of 15	ENSP00000381467.3	P45844-4
ABCG1	ENST00000361802.7	TSL:1	c.-11_-9dupGCC	5_prime_UTR	Exon 1 of 15	ENSP00000354995.2	P45844-1
ABCG1	ENST00000398457.6	TSL:1	c.49-6419_49-6417dupGCC	intron	N/A	ENSP00000381475.2	P45844-3

Frequencies

GnomAD3 genomes

AF:

0.00450

AC:

676

AN:

150178

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0134

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00132

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.00157

Gnomad SAS

AF:

0.00294

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00962

Gnomad NFE

AF:

0.00108

Gnomad OTH

AF:

0.00341

GnomAD2 exomes

AF:

0.00207

AC:

158

AN:

76150

AF XY:

0.00201

show subpopulations

Gnomad AFR exome

AF:

0.0109

Gnomad AMR exome

AF:

0.00212

Gnomad ASJ exome

AF:

0.00103

Gnomad EAS exome

AF:

0.000708

Gnomad FIN exome

AF:

0.000202

Gnomad NFE exome

AF:

0.00172

Gnomad OTH exome

AF:

0.00243

GnomAD4 exome

AF:

0.00133

AC:

1765

AN:

1322674

Hom.:

Cov.:

AF XY:

0.00133

AC XY:

866

AN XY:

653220

show subpopulations

African (AFR)

AF:

0.0138

AC:

375

AN:

27156

American (AMR)

AF:

0.00162

AC:

AN:

30208

Ashkenazi Jewish (ASJ)

AF:

0.000701

AC:

AN:

22818

East Asian (EAS)

AF:

0.000617

AC:

AN:

30786

South Asian (SAS)

AF:

0.00182

AC:

136

AN:

74926

European-Finnish (FIN)

AF:

0.000206

AC:

AN:

34008

Middle Eastern (MID)

AF:

0.00438

AC:

AN:

5250

European-Non Finnish (NFE)

AF:

0.000980

AC:

1022

AN:

1042794

Other (OTH)

AF:

0.00216

AC:

118

AN:

54728

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.403

Heterozygous variant carriers

131

197

262

328

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<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:

0.00449

AC:

675

AN:

150282

Hom.:

Cov.:

AF XY:

0.00430

AC XY:

316

AN XY:

73406

show subpopulations

African (AFR)

AF:

0.0133

AC:

548

AN:

41068

American (AMR)

AF:

0.00139

AC:

AN:

15126

Ashkenazi Jewish (ASJ)

AF:

0.000290

AC:

AN:

3448

East Asian (EAS)

AF:

0.00157

AC:

AN:

5080

South Asian (SAS)

AF:

0.00294

AC:

AN:

4764

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10190

Middle Eastern (MID)

AF:

0.0103

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.00108

AC:

AN:

67334

Other (OTH)

AF:

0.00337

AC:

AN:

2078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

122

152

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

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

ClinVar submissions

Significance:Benign

Revision:no assertion criteria provided

View on ClinVar

Pathogenic

VUS

Benign

Condition

ABCG1-related disorder (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.027

Mutation Taster

=300/0

polymorphism

(source)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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21-42219222-CCCGCCGCCGCCGCCGCCGCCG-CCCGCCGCCGCCGCCGCCGCCGCCG

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