rs745655298

Variant names:

• chr11-116820896-CCTGCTCCTGCTG-C
• rs745655298
• NM_000482.4:c.1150_1161delCAGCAGGAGCAG

Your query was ambiguous. Multiple possible variants found:

• chr11-116820896-CCTGCTCCTGCTG-C
• chr11-116820896-CCTGCTCCTGCTG-CCTGCTCCTGCTGCTGCTCCTGCTG

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP6_Moderate BS2

The NM_000482.4(APOA4):​c.1150_1161delCAGCAGGAGCAG​(p.Gln384_Gln387del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00019 in 1,613,294 control chromosomes in the GnomAD database, including 2 homozygotes. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.00096 (2 hom., cov: 33)
  • Exomes 𝑓: 0.00011 (0 hom.)
• Consequence: APOA4 NM_000482.4 conservative_inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.17
• Publications: 1 publications found

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]

ENSG00000285513 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -6 ACMG points.

• BP6: Variant 11-116820896-CCTGCTCCTGCTG-C is Benign according to our data. Variant chr11-116820896-CCTGCTCCTGCTG-C is described in ClinVar as [Likely_benign]. Clinvar id is 2059430.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOA4	NM_000482.4	c.1150_1161delCAGCAGGAGCAG	p.Gln384_Gln387del	conservative_inframe_deletion	Exon 3 of 3	ENST00000357780.5	NP_000473.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOA4	ENST00000357780.5	c.1150_1161delCAGCAGGAGCAG	p.Gln384_Gln387del	conservative_inframe_deletion	Exon 3 of 3	1	NM_000482.4	ENSP00000350425.3
ENSG00000285513	ENST00000645414.1	n.168+100_169-97delCTCCTGCTGCTG		intron_variant	Intron 1 of 1
ENSG00000305923	ENST00000814126.1	n.135+6572_135+6583delCTCCTGCTGCTG		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.000903 AC: 137 AN: 151706 Hom.: 1 Cov.: 33

Gnomad AFR AF: 0.00247

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00138

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.000118

Gnomad OTH AF: 0.00287

GnomAD2 exomes AF: 0.000267 AC: 67 AN: 250926 AF XY: 0.000199

Gnomad AFR exome AF: 0.00268

Gnomad AMR exome AF: 0.000377

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.0000544

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000792

Gnomad OTH exome AF: 0.000163

GnomAD4 exome AF: 0.000110 AC: 161 AN: 1461472 Hom.: 0 AF XY: 0.000111 AC XY: 81 AN XY: 727068

African (AFR) AF: 0.00208 AC: 69 AN: 33200

American (AMR) AF: 0.000380 AC: 17 AN: 44688

Ashkenazi Jewish (ASJ) AF: 0.0000383 AC: 1 AN: 26136

East Asian (EAS) AF: 0.0000756 AC: 3 AN: 39700

South Asian (SAS) AF: 0.0000116 AC: 1 AN: 86250

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53394

Middle Eastern (MID) AF: 0.00122 AC: 7 AN: 5758

European-Non Finnish (NFE) AF: 0.0000477 AC: 53 AN: 1111984

Other (OTH) AF: 0.000166 AC: 10 AN: 60362

GnomAD4 genome AF: 0.000955 AC: 145 AN: 151822 Hom.: 2 Cov.: 33 AF XY: 0.00102 AC XY: 76 AN XY: 74232

African (AFR) AF: 0.00246 AC: 101 AN: 41092

American (AMR) AF: 0.00137 AC: 21 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5188

South Asian (SAS) AF: 0.00 AC: 0 AN: 4832

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10618

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.000118 AC: 8 AN: 68018

Other (OTH) AF: 0.00664 AC: 14 AN: 2110

Alfa AF: 0.00 Hom.: 0

Bravo AF: 0.000910

EpiCase AF: 0.0000545

EpiControl AF: 0.000178

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Oct 22, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		2.2
Mutation Taster		=166/34	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs745655298; hg19: chr11-116691612;