11-116842914-C-G

Position:

• chr11-116842914-C-G

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+6675C>G 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 0.445 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 NR_126362.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.680

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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOA1-AS	NR_126362.1	n.123+6675C>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOA1-AS	ENST00000669664.1	n.74+6675C>G		intron_variant, non_coding_transcript_variant
APOA1-AS	ENST00000444200.1	n.123+6675C>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.133

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.558

Gnomad4 EAS AF: 0.218

Gnomad4 SAS AF: 0.305

Gnomad4 FIN AF: 0.538

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.480

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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