rs11216158

chr11-116840634-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_126362.1(APOA1-AS):n.123+4395G>A variant causes a intron, non coding transcript 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 NR_126362.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOA1-AS	NR_126362.1	n.123+4395G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOA1-AS	ENST00000669664.1	n.74+4395G>A		intron_variant, non_coding_transcript_variant
APOA1-AS	ENST00000444200.1	n.123+4395G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.266

Gnomad4 AMR AF: 0.204

Gnomad4 ASJ AF: 0.112

Gnomad4 EAS AF: 0.258

Gnomad4 SAS AF: 0.201

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.133

Gnomad4 OTH AF: 0.175

Alfa AF: 0.168 Hom.: 287

Bravo AF: 0.194

Asia WGS AF: 0.232 AC: 806 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.48
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11216158; hg19: chr11-116711350;