rs7301360

chr12-12789599-C-A

Variant summary

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

The NM_030817.3(APOLD1):c.*1947C>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 0.827 in 152,230 control chromosomes in the GnomAD database, including 52,198 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 0.83 (52198 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: APOLD1 NM_030817.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.118

Genes affected

APOLD1 (HGNC:25268): (apolipoprotein L domain containing 1) APOLD1 is an endothelial cell early response protein that may play a role in regulation of endothelial cell signaling and vascular function (Regard et al., 2004 [PubMed 15102925]).[supplied by OMIM, Dec 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.844 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APOLD1	NM_030817.3	c.*1947C>A		3_prime_UTR_variant	2/2	ENST00000356591.5
APOLD1	NM_001130415.2	c.*1947C>A		3_prime_UTR_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APOLD1	ENST00000356591.5	c.*1947C>A		3_prime_UTR_variant	2/2	1	NM_030817.3	P1

Frequencies

GnomAD3 genomes AF: 0.827 AC: 125858 AN: 152110 Hom.: 52156 Cov.: 33

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.840

Gnomad AMR AF: 0.816

Gnomad ASJ AF: 0.876

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.857

Gnomad MID AF: 0.880

Gnomad NFE AF: 0.850

Gnomad OTH AF: 0.826

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.500

GnomAD4 genome AF: 0.827 AC: 125959 AN: 152228 Hom.: 52198 Cov.: 33 AF XY: 0.829 AC XY: 61717 AN XY: 74426

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.816

Gnomad4 ASJ AF: 0.876

Gnomad4 EAS AF: 0.865

Gnomad4 SAS AF: 0.866

Gnomad4 FIN AF: 0.857

Gnomad4 NFE AF: 0.850

Gnomad4 OTH AF: 0.828

Alfa AF: 0.849 Hom.: 78108

Bravo AF: 0.819

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.42

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: rs7301360; hg19: chr12-12942533;