11-116842914-C-G

Variant names:

• chr11-116842914-C-G
• rs579163
• ENST00000444200.2:n.123+6675C>G

Variant summary

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

The ENST00000444200.2(APOA1-AS):​n.123+6675C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,080 control chromosomes in the GnomAD database, including 18,758 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 0.44 (18758 hom., cov: 32)
• Consequence: APOA1-AS ENST00000444200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680
• Publications: 2 publications found

Genes affected

APOA1-AS (HGNC:40079): (APOA1 antisense RNA)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444200.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOA1-AS	NR_126362.1		n.123+6675C>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOA1-AS	ENST00000444200.2	TSL:4	n.123+6675C>G		intron	N/A
	APOA1-AS	ENST00000669664.1		n.74+6675C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67666 AN: 151960 Hom.: 18761 Cov.: 32

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.558

Gnomad EAS AF: 0.218

Gnomad SAS AF: 0.304

Gnomad FIN AF: 0.538

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.445 AC: 67650 AN: 152080 Hom.: 18758 Cov.: 32 AF XY: 0.436 AC XY: 32447 AN XY: 74344

African (AFR) AF: 0.133 AC: 5524 AN: 41476

American (AMR) AF: 0.459 AC: 7022 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.558 AC: 1934 AN: 3468

East Asian (EAS) AF: 0.218 AC: 1130 AN: 5174

South Asian (SAS) AF: 0.305 AC: 1469 AN: 4822

European-Finnish (FIN) AF: 0.538 AC: 5687 AN: 10562

Middle Eastern (MID) AF: 0.476 AC: 140 AN: 294

European-Non Finnish (NFE) AF: 0.632 AC: 42991 AN: 67980

Other (OTH) AF: 0.480 AC: 1013 AN: 2110

Alfa AF: 0.371 Hom.: 1129

Bravo AF: 0.428

Asia WGS AF: 0.219 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.9
DANN	Benign	0.47
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs579163; hg19: chr11-116713630; COSMIC: COSV52613798;