3-195568790-C-T

Position:

• chr3-195568790-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700

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]

ACMG classification

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/exons	MANE	UniProt
APOD	NM_001647.4	c.*110G>A		3_prime_UTR_variant	5/5	ENST00000343267.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOD	ENST00000343267.8	c.*110G>A		3_prime_UTR_variant	5/5	1	NM_001647.4	P1
APOD	ENST00000458447.5	c.*475G>A		3_prime_UTR_variant, NMD_transcript_variant	6/6	2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 81170 AN: 143750 Hom.: 25884 Cov.: 26

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.: 8 AF XY: 0.650 AC XY: 213187 AN XY: 327814

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.: 26 AF XY: 0.566 AC XY: 39704 AN XY: 70156

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

Other links and lift over

dbSNP: rs7659; hg19: chr3-195295661; COSMIC: COSV58403037; COSMIC: COSV58403037;