chr11-116837697-C-T

Position:

• chr11-116837697-C-T

Variant summary

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

The ENST00000444200.1(APOA1-AS):​n.123+1458C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 563,690 control chromosomes in the GnomAD database, including 9,176 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 0.17 (2321 hom., cov: 32)
  • Exomes 𝑓: 0.18 (6855 hom.)
• Consequence: APOA1-AS ENST00000444200.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.304

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOA1-AS	NR_126362.1	n.123+1458C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOA1-AS	ENST00000444200.1	n.123+1458C>T		intron_variant		4
APOA1-AS	ENST00000669664.1	n.74+1458C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.172 AC: 26172 AN: 152058 Hom.: 2310 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.178

GnomAD4 exome AF: 0.177 AC: 72845 AN: 411514 Hom.: 6855 Cov.: 0 AF XY: 0.178 AC XY: 38205 AN XY: 214432

Gnomad4 AFR exome AF: 0.152

Gnomad4 AMR exome AF: 0.248

Gnomad4 ASJ exome AF: 0.148

Gnomad4 EAS exome AF: 0.207

Gnomad4 SAS exome AF: 0.195

Gnomad4 FIN exome AF: 0.189

Gnomad4 NFE exome AF: 0.167

Gnomad4 OTH exome AF: 0.182

GnomAD4 genome AF: 0.172 AC: 26224 AN: 152176 Hom.: 2321 Cov.: 32 AF XY: 0.174 AC XY: 12950 AN XY: 74392

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.220

Gnomad4 ASJ AF: 0.148

Gnomad4 EAS AF: 0.254

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.190

Gnomad4 NFE AF: 0.166

Gnomad4 OTH AF: 0.182

Alfa AF: 0.0954 Hom.: 132

Bravo AF: 0.177

Asia WGS AF: 0.222 AC: 770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.2
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs670; hg19: chr11-116708413;