rs613808

chr11-116840252-A-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+4013A>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 0.511 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 NR_126362.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.556

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=-0.85).
• 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/exons	MANE	UniProt
APOA1-AS	NR_126362.1	n.123+4013A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOA1-AS	ENST00000669664.1	n.74+4013A>G		intron_variant, non_coding_transcript_variant
APOA1-AS	ENST00000444200.1	n.123+4013A>G		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.280

Gnomad4 SAS AF: 0.421

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.538

Alfa AF: 0.534 Hom.: 3555

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs613808; hg19: chr11-116710968;