11-116839523-G-T

Position:

• chr11-116839523-G-T

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+3284G>T 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 0.0551 in 152,246 control chromosomes in the GnomAD database, including 483 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 0.055 (483 hom., cov: 33)
• Consequence: APOA1-AS NR_126362.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.580

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOA1-AS	NR_126362.1	n.123+3284G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOA1-AS	ENST00000669664.1	n.74+3284G>T		intron_variant, non_coding_transcript_variant
APOA1-AS	ENST00000444200.1	n.123+3284G>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.0550 AC: 8373 AN: 152128 Hom.: 482 Cov.: 33

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0291

Gnomad ASJ AF: 0.0144

Gnomad EAS AF: 0.0820

Gnomad SAS AF: 0.0195

Gnomad FIN AF: 0.0126

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0168

Gnomad OTH AF: 0.0497

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

GnomAD4 genome AF: 0.0551 AC: 8387 AN: 152246 Hom.: 483 Cov.: 33 AF XY: 0.0546 AC XY: 4065 AN XY: 74448

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.0291

Gnomad4 ASJ AF: 0.0144

Gnomad4 EAS AF: 0.0826

Gnomad4 SAS AF: 0.0197

Gnomad4 FIN AF: 0.0126

Gnomad4 NFE AF: 0.0168

Gnomad4 OTH AF: 0.0501

Alfa AF: 0.0147 Hom.: 5

Bravo AF: 0.0606

Asia WGS AF: 0.0670 AC: 234 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.084
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs632153; hg19: chr11-116710239;