Genetic Variant APOD:c.*110G>A (chr3-195568790-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001647.4(APOD):c.*110G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 762,516 control chromosomes in the GnomAD database, including 164,886 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 0.56 ( 25897 hom., cov: 26)

Exomes 𝑓: 0.66 ( 138989 hom. )

Consequence

APOD
NM_001647.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00700

Variant links:

Genes affected

APOD (HGNC:612): (apolipoprotein D) This gene encodes a component of high density lipoprotein that has no marked similarity to other apolipoprotein sequences. It has a high degree of homology to plasma retinol-binding protein and other members of the alpha 2 microglobulin protein superfamily of carrier proteins, also known as lipocalins. This glycoprotein is closely associated with the enzyme lecithin:cholesterol acyltransferase - an enzyme involved in lipoprotein metabolism. [provided by RefSeq, Aug 2008]

APOD links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOD	NM_001647.4 link	c.*110G>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000343267.8	NP_001638.1	P05090

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOD	ENST00000343267 link	c.*110G>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_001647.4	ENSP00000345179.3		P05090

Frequencies

GnomAD3 genomes

AF:

0.565

AC:

81170

AN:

143750

Hom.:

25884

Cov.:

show subpopulations

Gnomad AFR

AF:

0.214

Gnomad AMI

AF:

0.787

Gnomad AMR

AF:

0.713

Gnomad ASJ

AF:

0.714

Gnomad EAS

AF:

0.522

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.749

Gnomad MID

AF:

0.571

Gnomad NFE

AF:

0.686

Gnomad OTH

AF:

0.610

GnomAD4 exome

AF:

0.658

AC:

406979

AN:

618704

Hom.:

138989

Cov.:

AF XY:

0.650

AC XY:

213187

AN XY:

327814

show subpopulations

Gnomad4 AFR exome

AF:

0.187

Gnomad4 AMR exome

AF:

0.786

Gnomad4 ASJ exome

AF:

0.721

Gnomad4 EAS exome

AF:

0.532

Gnomad4 SAS exome

AF:

0.487

Gnomad4 FIN exome

AF:

0.725

Gnomad4 NFE exome

AF:

0.696

Gnomad4 OTH exome

AF:

0.631

GnomAD4 genome

AF:

0.565

AC:

81194

AN:

143812

Hom.:

25897

Cov.:

AF XY:

0.566

AC XY:

39704

AN XY:

70156

show subpopulations

Gnomad4 AFR

AF:

0.214

Gnomad4 AMR

AF:

0.714

Gnomad4 ASJ

AF:

0.714

Gnomad4 EAS

AF:

0.522

Gnomad4 SAS

AF:

0.491

Gnomad4 FIN

AF:

0.749

Gnomad4 NFE

AF:

0.686

Gnomad4 OTH

AF:

0.611

Alfa

AF:

0.612

Hom.:

8208

Bravo

AF:

0.524

Asia WGS

AF:

0.514

AC:

1792

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.7

DANN

Benign

0.64

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over