rs7301360

Variant names:

• chr12-12789599-C-A
• rs7301360
• NM_030817.3:c.*1947C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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]

APOLD1 Gene-Disease associations (from GenCC):

• inherited blood coagulation disorder

  Inheritance: AD Classification: LIMITED Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_030817.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOLD1	NM_030817.3	MANE Select	c.*1947C>A		3_prime_UTR	Exon 2 of 2	NP_110444.3	A0AVN6
	APOLD1	NM_001130415.2		c.*1947C>A		3_prime_UTR	Exon 2 of 2	NP_001123887.1	Q96LR9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APOLD1	ENST00000356591.5	TSL:1 MANE Select	c.*1947C>A		3_prime_UTR	Exon 2 of 2	ENSP00000348998.4	Q96LR9-2
	APOLD1	ENST00000326765.10	TSL:1	c.*1947C>A		3_prime_UTR	Exon 2 of 2	ENSP00000324277.6	Q96LR9-1
	APOLD1	ENST00000895456.1		c.*1947C>A		3_prime_UTR	Exon 2 of 2	ENSP00000565515.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.500 AC: 1 AN: 2

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.773 AC: 32090 AN: 41494

American (AMR) AF: 0.816 AC: 12493 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.876 AC: 3042 AN: 3472

East Asian (EAS) AF: 0.865 AC: 4494 AN: 5196

South Asian (SAS) AF: 0.866 AC: 4167 AN: 4814

European-Finnish (FIN) AF: 0.857 AC: 9083 AN: 10598

Middle Eastern (MID) AF: 0.878 AC: 258 AN: 294

European-Non Finnish (NFE) AF: 0.850 AC: 57815 AN: 68028

Other (OTH) AF: 0.828 AC: 1751 AN: 2116

Alfa AF: 0.846 Hom.: 107739

Bravo AF: 0.819

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.0
DANN	Benign	0.42
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7301360; hg19: chr12-12942533;