Variant 21-42219222-CCCG-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_016818.3(ABCG1):c.-11_-9del variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0127 in 1,371,458 control chromosomes in the GnomAD database, including 483 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.035 ( 284 hom., cov: 26)

Exomes 𝑓: 0.010 ( 199 hom. )

Consequence

ABCG1
NM_016818.3 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.18

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 made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 21-42219222-CCCG-C is Benign according to our data. Variant chr21-42219222-CCCG-C is described in ClinVar as [Benign]. Clinvar id is 3059271.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.104 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCG1	NM_016818.3 linkuse as main transcript	c.-11_-9del		5_prime_UTR_variant	1/15	ENST00000398449.8
LOC105372814	XR_937748.4 linkuse as main transcript	n.121+925_121+927del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCG1	ENST00000398449.8 linkuse as main transcript	c.-11_-9del		5_prime_UTR_variant	1/15	1	NM_016818.3	P1	P45844-4

Frequencies

GnomAD3 genomes

AF:

0.0344

AC:

5158

AN:

150108

Hom.:

281

Cov.:

show subpopulations

Gnomad AFR

AF:

0.106

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0450

Gnomad ASJ

AF:

0.000290

Gnomad EAS

AF:

0.000196

Gnomad SAS

AF:

0.00356

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0224

Gnomad NFE

AF:

0.000847

Gnomad OTH

AF:

0.0258

GnomAD3 exomes

AF:

0.0350

AC:

2669

AN:

76150

Hom.:

AF XY:

0.0309

AC XY:

1317

AN XY:

42682

show subpopulations

Gnomad AFR exome

AF:

0.179

Gnomad AMR exome

AF:

0.0883

Gnomad ASJ exome

AF:

0.0107

Gnomad EAS exome

AF:

0.0264

Gnomad SAS exome

AF:

0.0156

Gnomad FIN exome

AF:

0.00847

Gnomad NFE exome

AF:

0.0177

Gnomad OTH exome

AF:

0.0306

GnomAD4 exome

AF:

0.0101

AC:

12283

AN:

1221246

Hom.:

199

AF XY:

0.00947

AC XY:

5688

AN XY:

600720

show subpopulations

Gnomad4 AFR exome

AF:

0.129

Gnomad4 AMR exome

AF:

0.0676

Gnomad4 ASJ exome

AF:

0.00756

Gnomad4 EAS exome

AF:

0.00855

Gnomad4 SAS exome

AF:

0.00950

Gnomad4 FIN exome

AF:

0.00623

Gnomad4 NFE exome

AF:

0.00520

Gnomad4 OTH exome

AF:

0.0164

GnomAD4 genome

AF:

0.0346

AC:

5194

AN:

150212

Hom.:

284

Cov.:

AF XY:

0.0339

AC XY:

2488

AN XY:

73362

show subpopulations

Gnomad4 AFR

AF:

0.107

Gnomad4 AMR

AF:

0.0453

Gnomad4 ASJ

AF:

0.000290

Gnomad4 EAS

AF:

0.000197

Gnomad4 SAS

AF:

0.00315

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000847

Gnomad4 OTH

AF:

0.0275

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

ABCG1-related disorder

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 19, 2019

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over