rs2280520

Variant summary

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

The NM_001647.4(APOD):​c.123+327C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 152,134 control chromosomes in the GnomAD database, including 1,843 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 0.14 ( 1843 hom., cov: 31)

Consequence

APOD
NM_001647.4 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.210
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]

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=-0.81).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
APODNM_001647.4 linkuse as main transcriptc.123+327C>T intron_variant ENST00000343267.8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
APODENST00000343267.8 linkuse as main transcriptc.123+327C>T intron_variant 1 NM_001647.4 P1

Frequencies

GnomAD3 genomes
AF:
0.139
AC:
21136
AN:
152016
Hom.:
1840
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.0940
Gnomad AMI
AF:
0.137
Gnomad AMR
AF:
0.105
Gnomad ASJ
AF:
0.178
Gnomad EAS
AF:
0.413
Gnomad SAS
AF:
0.280
Gnomad FIN
AF:
0.151
Gnomad MID
AF:
0.155
Gnomad NFE
AF:
0.140
Gnomad OTH
AF:
0.137
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.139
AC:
21143
AN:
152134
Hom.:
1843
Cov.:
31
AF XY:
0.143
AC XY:
10627
AN XY:
74366
show subpopulations
Gnomad4 AFR
AF:
0.0941
Gnomad4 AMR
AF:
0.104
Gnomad4 ASJ
AF:
0.178
Gnomad4 EAS
AF:
0.413
Gnomad4 SAS
AF:
0.278
Gnomad4 FIN
AF:
0.151
Gnomad4 NFE
AF:
0.140
Gnomad4 OTH
AF:
0.140
Alfa
AF:
0.134
Hom.:
304
Bravo
AF:
0.136
Asia WGS
AF:
0.309
AC:
1074
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.81
CADD
Benign
5.0
DANN
Benign
0.49

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.

Other links and lift over

dbSNP: rs2280520; hg19: chr3-195305883; API