11-116820795-GGACA-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_000482.4(APOA4):c.*68_*71del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.489 in 1,577,418 control chromosomes in the GnomAD database, including 197,947 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.39 (13398 hom., cov: 0)
  • Exomes 𝑓: 0.50 (184549 hom.)
• Consequence: APOA4 NM_000482.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.937

Genes affected

APOA4 (HGNC:602): (apolipoprotein A4) Apoliprotein (apo) A-IV gene contains 3 exons separated by two introns. A sequence polymorphism has been identified in the 3'UTR of the third exon. The primary translation product is a 396-residue preprotein which after proteolytic processing is secreted its primary site of synthesis, the intestine, in association with chylomicron particles. Although its precise function is not known, apo A-IV is a potent activator of lecithin-cholesterol acyltransferase in vitro. [provided by RefSeq, Jul 2008]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 11-116820795-GGACA-G is Benign according to our data. Variant chr11-116820795-GGACA-G is described in ClinVar as [Benign]. Clinvar id is 1238294.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOA4	NM_000482.4	c.*68_*71del		3_prime_UTR_variant	3/3	ENST00000357780.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOA4	ENST00000357780.5	c.*68_*71del		3_prime_UTR_variant	3/3	1	NM_000482.4	P1
	ENST00000645414.1	n.165_168del		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.387 AC: 58724 AN: 151762 Hom.: 13406 Cov.: 0

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.292

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.457

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.406

GnomAD4 exome AF: 0.500 AC: 712397 AN: 1425540 Hom.: 184549 AF XY: 0.494 AC XY: 348997 AN XY: 705810

Gnomad4 AFR exome AF: 0.122

Gnomad4 AMR exome AF: 0.473

Gnomad4 ASJ exome AF: 0.411

Gnomad4 EAS exome AF: 0.270

Gnomad4 SAS exome AF: 0.319

Gnomad4 FIN exome AF: 0.467

Gnomad4 NFE exome AF: 0.540

Gnomad4 OTH exome AF: 0.460

GnomAD4 genome AF: 0.387 AC: 58715 AN: 151878 Hom.: 13398 Cov.: 0 AF XY: 0.381 AC XY: 28251 AN XY: 74240

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.433

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.312

Gnomad4 FIN AF: 0.457

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.404

Bravo AF: 0.382

Asia WGS AF: 0.276 AC: 963 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 10, 2021

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Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs2234669; hg19: chr11-116691511;