rs2278357

Positions:

• chr2-43812700-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_022436.3(ABCG5):​c.*416G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.203 in 202,312 control chromosomes in the GnomAD database, including 5,029 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.22 (4279 hom., cov: 32)
  • Exomes 𝑓: 0.16 (750 hom.)
• Consequence: ABCG5 NM_022436.3 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.86

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP6: Variant 2-43812700-C-T is Benign according to our data. Variant chr2-43812700-C-T is described in ClinVar as [Benign]. Clinvar id is 336029.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.334 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ABCG5	NM_022436.3	c.*416G>A		3_prime_UTR_variant	13/13	ENST00000405322.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ABCG5	ENST00000405322.8	c.*416G>A		3_prime_UTR_variant	13/13	1	NM_022436.3	P1
ABCG5	ENST00000486512.5	n.2893G>A		non_coding_transcript_exon_variant	9/9	1
ABCG5	ENST00000644754.1	n.2756G>A		non_coding_transcript_exon_variant	10/10

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33312 AN: 152020 Hom.: 4266 Cov.: 32

Gnomad AFR AF: 0.339

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.263

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.202

GnomAD4 exome AF: 0.155 AC: 7791 AN: 50174 Hom.: 750 Cov.: 0 AF XY: 0.156 AC XY: 4013 AN XY: 25650

Gnomad4 AFR exome AF: 0.262

Gnomad4 AMR exome AF: 0.306

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.0962

Gnomad4 SAS exome AF: 0.220

Gnomad4 FIN exome AF: 0.109

Gnomad4 NFE exome AF: 0.132

Gnomad4 OTH exome AF: 0.134

GnomAD4 genome AF: 0.219 AC: 33358 AN: 152138 Hom.: 4279 Cov.: 32 AF XY: 0.219 AC XY: 16289 AN XY: 74382

Gnomad4 AFR AF: 0.339

Gnomad4 AMR AF: 0.276

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.113

Gnomad4 SAS AF: 0.262

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.157

Gnomad4 OTH AF: 0.203

Alfa AF: 0.177 Hom.: 3601

Bravo AF: 0.235

Asia WGS AF: 0.185 AC: 645 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Sitosterolemia 1 Benign:1

Benign, 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 and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.25
DANN	Benign	0.65

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: rs2278357; hg19: chr2-44039839;