chr2-43812831-C-G

Position:

• chr2-43812831-C-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 BS1 BS2

The NM_022436.3(ABCG5):​c.*285G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00672 in 370,858 control chromosomes in the GnomAD database, including 16 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.0064 (3 hom., cov: 32)
  • Exomes 𝑓: 0.0069 (13 hom.)
• Consequence: ABCG5 NM_022436.3 3_prime_UTR
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1 B:2
• Conservation: PhyloP100: -0.462

Genes affected

ABCG5 (HGNC:13886): (ATP binding cassette subfamily G member 5) 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. The protein encoded by this gene functions as a half-transporter to limit intestinal absorption and promote biliary excretion of sterols. It is expressed in a tissue-specific manner in the liver, colon, and intestine. This gene is tandemly arrayed on chromosome 2, in a head-to-head orientation with family member ABCG8. Mutations in this gene may contribute to sterol accumulation and atheroschlerosis, and have been observed in patients with sitosterolemia. [provided by RefSeq, Jul 2008]

DYNC2LI1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-43812831-C-G is Benign according to our data. Variant chr2-43812831-C-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 336033.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=1}.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00643 (979/152230) while in subpopulation NFE AF= 0.00956 (650/68020). AF 95% confidence interval is 0.00895. There are 3 homozygotes in gnomad4. There are 458 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCG5	NM_022436.3	c.*285G>C		3_prime_UTR_variant	13/13	ENST00000405322.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCG5	ENST00000405322.8	c.*285G>C		3_prime_UTR_variant	13/13	1	NM_022436.3	P1
ABCG5	ENST00000486512.5	n.2762G>C		non_coding_transcript_exon_variant	9/9	1
ABCG5	ENST00000644754.1	n.2625G>C		non_coding_transcript_exon_variant	10/10
ABCG5	ENST00000409962.1			downstream_gene_variant		2

Frequencies

GnomAD3 genomes AF: 0.00644 AC: 979 AN: 152112 Hom.: 3 Cov.: 32

Gnomad AFR AF: 0.00188

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00649

Gnomad ASJ AF: 0.000577

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.00664

Gnomad FIN AF: 0.00971

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00955

Gnomad OTH AF: 0.00621

GnomAD4 exome AF: 0.00693 AC: 1514 AN: 218628 Hom.: 13 Cov.: 0 AF XY: 0.00672 AC XY: 760 AN XY: 113146

Gnomad4 AFR exome AF: 0.00121

Gnomad4 AMR exome AF: 0.00427

Gnomad4 ASJ exome AF: 0.000414

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00731

Gnomad4 FIN exome AF: 0.00851

Gnomad4 NFE exome AF: 0.00837

Gnomad4 OTH exome AF: 0.00649

GnomAD4 genome AF: 0.00643 AC: 979 AN: 152230 Hom.: 3 Cov.: 32 AF XY: 0.00615 AC XY: 458 AN XY: 74424

Gnomad4 AFR AF: 0.00188

Gnomad4 AMR AF: 0.00648

Gnomad4 ASJ AF: 0.000577

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.00664

Gnomad4 FIN AF: 0.00971

Gnomad4 NFE AF: 0.00956

Gnomad4 OTH AF: 0.00615

Alfa AF: 0.00337 Hom.: 0

Bravo AF: 0.00524

Asia WGS AF: 0.00231 AC: 8 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:1 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Benign:2

Likely benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 10, 2018	- -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Feb 01, 2023	ABCG5: BS2 -

Sitosterolemia 1 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jan 13, 2018

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.2
DANN	Benign	0.57

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

Other links and lift over

dbSNP: rs114868704; hg19: chr2-44039970;