11-116840634-G-A

Variant names:

• chr11-116840634-G-A
• rs11216158
• ENST00000444200.2:n.123+4395G>A

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+4395G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.182 in 152,236 control chromosomes in the GnomAD database, including 2,835 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 0.18 (2835 hom., cov: 33)
• Consequence: APOA1-AS ENST00000444200.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• Publications: 9 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.262 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+4395G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOA1-AS	ENST00000444200.2	TSL:4	n.123+4395G>A		intron	N/A
	APOA1-AS	ENST00000669664.1		n.74+4395G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.182 AC: 27616 AN: 152118 Hom.: 2817 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.133

Gnomad AMR AF: 0.204

Gnomad ASJ AF: 0.112

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.133

Gnomad OTH AF: 0.172

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

GnomAD4 genome AF: 0.182 AC: 27692 AN: 152236 Hom.: 2835 Cov.: 33 AF XY: 0.181 AC XY: 13470 AN XY: 74450

African (AFR) AF: 0.266 AC: 11048 AN: 41540

American (AMR) AF: 0.204 AC: 3120 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.112 AC: 389 AN: 3472

East Asian (EAS) AF: 0.258 AC: 1338 AN: 5178

South Asian (SAS) AF: 0.201 AC: 970 AN: 4828

European-Finnish (FIN) AF: 0.119 AC: 1266 AN: 10610

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.133 AC: 9014 AN: 67994

Other (OTH) AF: 0.175 AC: 370 AN: 2112

Alfa AF: 0.157 Hom.: 3039

Bravo AF: 0.194

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.48
DANN	Benign	0.49
PhyloP100		-0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11216158;

hg19: chr11-116711350;