NM_022437.3:c.1488+89T>C

Variant names:

• chr2-43874572-T-C
• rs13405698
• NM_022437.3:c.1488+89T>C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_022437.3(ABCG8):​c.1488+89T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 1,104,180 control chromosomes in the GnomAD database, including 37,859 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.23 (4257 hom., cov: 31)
  • Exomes 𝑓: 0.26 (33602 hom.)
• Consequence: ABCG8 NM_022437.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -0.179
• Publications: 4 publications found

Genes affected

ABCG8 (HGNC:13887): (ATP binding cassette subfamily G member 8) 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 to exclude non-cholesterol sterol entry at the intestinal level, promote excretion of cholesterol and sterols into bile, and to facilitate transport of sterols back into the intestinal lumen. It is expressed in a tissue-specific manner in the liver, intestine, and gallbladder. This gene is tandemly arrayed on chromosome 2, in a head-to-head orientation with family member ABCG5. Mutations in this gene may contribute to sterol accumulation and atherosclerosis, and have been observed in patients with sitosterolemia. [provided by RefSeq, Jul 2008]

ABCG8 Gene-Disease associations (from GenCC):

• sitosterolemia

  Inheritance: AR Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, Illumina
• sitosterolemia 1

  Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P

ACMG classification

Our verdict: Benign. The variant received -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BP6: Variant 2-43874572-T-C is Benign according to our data. Variant chr2-43874572-T-C is described in ClinVar as Benign. ClinVar VariationId is 1229584.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.264 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022437.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCG8	NM_022437.3	MANE Select	c.1488+89T>C		intron	N/A	NP_071882.1
	ABCG8	NM_001357321.2		c.1485+89T>C		intron	N/A	NP_001344250.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ABCG8	ENST00000272286.4	TSL:1 MANE Select	c.1488+89T>C		intron	N/A	ENSP00000272286.2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34679 AN: 151834 Hom.: 4254 Cov.: 31

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.157

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0178

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.267

Gnomad OTH AF: 0.230

GnomAD4 exome AF: 0.257 AC: 244731 AN: 952228 Hom.: 33602 AF XY: 0.260 AC XY: 128776 AN XY: 495606

African (AFR) AF: 0.213 AC: 5003 AN: 23510

American (AMR) AF: 0.118 AC: 5190 AN: 43798

Ashkenazi Jewish (ASJ) AF: 0.321 AC: 7385 AN: 23008

East Asian (EAS) AF: 0.0133 AC: 497 AN: 37304

South Asian (SAS) AF: 0.276 AC: 20998 AN: 75974

European-Finnish (FIN) AF: 0.263 AC: 13786 AN: 52346

Middle Eastern (MID) AF: 0.314 AC: 1461 AN: 4650

European-Non Finnish (NFE) AF: 0.277 AC: 179608 AN: 647846

Other (OTH) AF: 0.247 AC: 10803 AN: 43792

GnomAD4 genome AF: 0.228 AC: 34698 AN: 151952 Hom.: 4257 Cov.: 31 AF XY: 0.228 AC XY: 16963 AN XY: 74250

African (AFR) AF: 0.200 AC: 8294 AN: 41430

American (AMR) AF: 0.157 AC: 2396 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1070 AN: 3468

East Asian (EAS) AF: 0.0182 AC: 94 AN: 5162

South Asian (SAS) AF: 0.254 AC: 1220 AN: 4804

European-Finnish (FIN) AF: 0.256 AC: 2698 AN: 10538

Middle Eastern (MID) AF: 0.320 AC: 94 AN: 294

European-Non Finnish (NFE) AF: 0.267 AC: 18144 AN: 67950

Other (OTH) AF: 0.228 AC: 481 AN: 2108

Alfa AF: 0.209 Hom.: 1452

Bravo AF: 0.219

Asia WGS AF: 0.131 AC: 457 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Jul 09, 2018

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.7
DANN	Benign	0.69
PhyloP100		-0.18
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13405698; hg19: chr2-44101711;