Variant chr3-195573869-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001647.4(APOD):c.226G>A(p.Val76Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,614,200 control chromosomes in the GnomAD database, including 166 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0092 ( 15 hom., cov: 32)

Exomes 𝑓: 0.012 ( 151 hom. )

Consequence

APOD
NM_001647.4 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 3.46

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 -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00900656).

BP6

Variant 3-195573869-C-T is Benign according to our data. Variant chr3-195573869-C-T is described in ClinVar as [Benign]. Clinvar id is 2654366.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 15 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOD	NM_001647.4 linkuse as main transcript	c.226G>A	p.Val76Met	missense_variant	3/5	ENST00000343267.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOD	ENST00000343267.8 linkuse as main transcript	c.226G>A	p.Val76Met	missense_variant	3/5	1	NM_001647.4	P1

Frequencies

GnomAD3 genomes

AF:

0.00918

AC:

1397

AN:

152230

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00239

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00648

Gnomad ASJ

AF:

0.0133

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00207

Gnomad FIN

AF:

0.0175

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0137

Gnomad OTH

AF:

0.0105

GnomAD3 exomes

AF:

0.00953

AC:

2395

AN:

251418

Hom.:

AF XY:

0.00967

AC XY:

1314

AN XY:

135874

show subpopulations

Gnomad AFR exome

AF:

0.00191

Gnomad AMR exome

AF:

0.00561

Gnomad ASJ exome

AF:

0.0104

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00265

Gnomad FIN exome

AF:

0.0167

Gnomad NFE exome

AF:

0.0135

Gnomad OTH exome

AF:

0.0135

GnomAD4 exome

AF:

0.0120

AC:

17497

AN:

1461852

Hom.:

151

Cov.:

AF XY:

0.0117

AC XY:

8527

AN XY:

727232

show subpopulations

Gnomad4 AFR exome

AF:

0.00176

Gnomad4 AMR exome

AF:

0.00608

Gnomad4 ASJ exome

AF:

0.00987

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00238

Gnomad4 FIN exome

AF:

0.0163

Gnomad4 NFE exome

AF:

0.0136

Gnomad4 OTH exome

AF:

0.0107

GnomAD4 genome

AF:

0.00917

AC:

1397

AN:

152348

Hom.:

Cov.:

AF XY:

0.00969

AC XY:

722

AN XY:

74496

show subpopulations

Gnomad4 AFR

AF:

0.00238

Gnomad4 AMR

AF:

0.00647

Gnomad4 ASJ

AF:

0.0133

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00207

Gnomad4 FIN

AF:

0.0175

Gnomad4 NFE

AF:

0.0137

Gnomad4 OTH

AF:

0.0104

Alfa

AF:

0.0119

Hom.:

Bravo

AF:

0.00811

TwinsUK

AF:

0.0140

AC:

ALSPAC

AF:

0.0174

AC:

ESP6500AA

AF:

0.00182

AC:

ESP6500EA

AF:

0.0140

AC:

120

ExAC

AF:

0.0101

AC:

1226

Asia WGS

AF:

0.00202

AC:

AN:

3478

EpiCase

AF:

0.0139

EpiControl

AF:

0.0130

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Jan 01, 2023

APOD: BS1, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Pathogenic

0.92

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.24

CADD

Uncertain

DANN

Uncertain

1.0

DEOGEN2

Benign

0.36

T;.;T

Eigen

Pathogenic

0.85

Eigen_PC

Pathogenic

0.71

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.85

T;D;T

MetaRNN

Benign

0.0090

T;T;T

MetaSVM

Uncertain

0.22

MutationAssessor

Pathogenic

3.9

H;.;.

MutationTaster

Benign

1.0

PrimateAI

Uncertain

0.54

PROVEAN

Uncertain

-2.8

D;D;D

REVEL

Uncertain

0.39

Sift

Uncertain

0.0020

D;D;D

Sift4G

Uncertain

0.0020

D;.;.

Polyphen

1.0

D;.;.

Vest4

0.81

MPC

0.60

ClinPred

0.075

GERP RS

5.7

Varity_R

0.87

gMVP

0.68

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over