rs613808

Variant names:

• chr11-116840252-A-G
• rs613808
• ENST00000444200.2:n.123+4013A>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+4013A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.511 in 152,252 control chromosomes in the GnomAD database, including 23,565 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 0.51 (23565 hom., cov: 34)
• Consequence: APOA1-AS ENST00000444200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556
• Publications: 15 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=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA1-AS	NR_126362.1	n.123+4013A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOA1-AS	ENST00000444200.2	n.123+4013A>G		intron_variant	Intron 1 of 1	4
APOA1-AS	ENST00000669664.1	n.74+4013A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.511 AC: 77748 AN: 152134 Hom.: 23575 Cov.: 34

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.846

Gnomad AMR AF: 0.508

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.281

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.511 AC: 77733 AN: 152252 Hom.: 23565 Cov.: 34 AF XY: 0.503 AC XY: 37451 AN XY: 74430

African (AFR) AF: 0.198 AC: 8236 AN: 41558

American (AMR) AF: 0.507 AC: 7751 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2308 AN: 3472

East Asian (EAS) AF: 0.280 AC: 1450 AN: 5176

South Asian (SAS) AF: 0.421 AC: 2032 AN: 4822

European-Finnish (FIN) AF: 0.614 AC: 6499 AN: 10590

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47372 AN: 68014

Other (OTH) AF: 0.538 AC: 1137 AN: 2114

Alfa AF: 0.513 Hom.: 7098

Bravo AF: 0.492

Asia WGS AF: 0.311 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.3
DANN	Benign	0.79
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs613808; hg19: chr11-116710968; COSMIC: COSV107247741;