11-116840425-C-T

Variant names:

• chr11-116840425-C-T
• rs2727784
• ENST00000444200.2:n.123+4186C>T

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+4186C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.466 in 152,126 control chromosomes in the GnomAD database, including 19,506 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 0.47 (19506 hom., cov: 33)
• Consequence: APOA1-AS ENST00000444200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.453
• Publications: 14 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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA1-AS	NR_126362.1	n.123+4186C>T		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+4186C>T		intron_variant	Intron 1 of 1	4
APOA1-AS	ENST00000669664.1	n.74+4186C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.467 AC: 70940 AN: 152006 Hom.: 19518 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.803

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.624

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.401

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.628

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.466 AC: 70926 AN: 152126 Hom.: 19506 Cov.: 33 AF XY: 0.460 AC XY: 34196 AN XY: 74390

African (AFR) AF: 0.187 AC: 7766 AN: 41510

American (AMR) AF: 0.473 AC: 7237 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.624 AC: 2163 AN: 3466

East Asian (EAS) AF: 0.265 AC: 1368 AN: 5158

South Asian (SAS) AF: 0.401 AC: 1931 AN: 4816

European-Finnish (FIN) AF: 0.552 AC: 5844 AN: 10594

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.628 AC: 42661 AN: 67976

Other (OTH) AF: 0.502 AC: 1059 AN: 2110

Alfa AF: 0.543 Hom.: 34433

Bravo AF: 0.452

Asia WGS AF: 0.301 AC: 1054 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.0
DANN	Benign	0.48
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs2727784; hg19: chr11-116711141;