rs3760291

Variant names:

• chr17-66230079-G-T
• rs3760291
• ENST00000577982.1:c.-43-657C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577982.1(APOH):​c.-43-657C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.174 in 148,922 control chromosomes in the GnomAD database, including 2,820 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.17 (2820 hom., cov: 31)
• Consequence: APOH ENST00000577982.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 4 publications found

Genes affected

APOH (HGNC:616): (apolipoprotein H) Apolipoprotein H, also known as beta-2-glycoprotein I, is a component of circulating plasma lipoproteins. It has been implicated in a variety of physiologic pathways including lipoprotein metabolism, coagulation, hemostasis, and the production of antiphospholipid autoantibodies. APOH may be a required cofactor for anionic phospholipid binding by the antiphospholipid autoantibodies found in sera of many patients with lupus and primary antiphospholipid syndrome (APS). The anti-beta (2) glycoprotein I antibodies from APS patients, mediate inhibition of activated protein C which has anticoagulant properties. Because beta-2-GPI is the main autoantigen in patients with APS, the disruption of this pathway by autoantibodies may be an important mechanism for thrombosis in patients with APS.[provided by RefSeq, Dec 2019]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOH	ENST00000577982.1	c.-43-657C>A		intron_variant	Intron 1 of 5	5		ENSP00000464301.1

Frequencies

GnomAD3 genomes AF: 0.174 AC: 25839 AN: 148804 Hom.: 2820 Cov.: 31

Gnomad AFR AF: 0.0690

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0684

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.109

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.154

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.174 AC: 25840 AN: 148922 Hom.: 2820 Cov.: 31 AF XY: 0.167 AC XY: 12136 AN XY: 72568

African (AFR) AF: 0.0689 AC: 2732 AN: 39676

American (AMR) AF: 0.123 AC: 1818 AN: 14830

Ashkenazi Jewish (ASJ) AF: 0.146 AC: 503 AN: 3454

East Asian (EAS) AF: 0.0685 AC: 335 AN: 4890

South Asian (SAS) AF: 0.0682 AC: 315 AN: 4620

European-Finnish (FIN) AF: 0.205 AC: 2128 AN: 10376

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.256 AC: 17346 AN: 67796

Other (OTH) AF: 0.153 AC: 319 AN: 2084

Alfa AF: 0.207 Hom.: 605

Bravo AF: 0.160

Asia WGS AF: 0.0650 AC: 230 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.1
DANN	Benign	0.31
PhyloP100		-0.036

Splicing

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

Other links and lift over

dbSNP: rs3760291; hg19: chr17-64226197;