rs2110597

Positions:

• chr12-12788079-G-A

Variant summary

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

The NM_030817.3(APOLD1):​c.*427G>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 0.595 in 161,720 control chromosomes in the GnomAD database, including 29,533 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 0.59 (27456 hom., cov: 31)
  • Exomes 𝑓: 0.64 (2077 hom.)
• Consequence: APOLD1 NM_030817.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.617

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 (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.695 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOLD1	NM_030817.3	c.*427G>A		3_prime_UTR_variant	2/2	ENST00000356591.5	NP_110444.3
APOLD1	NM_001130415.2	c.*427G>A		3_prime_UTR_variant	2/2		NP_001123887.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOLD1	ENST00000356591.5	c.*427G>A		3_prime_UTR_variant	2/2	1	NM_030817.3	ENSP00000348998.4

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89918 AN: 151918 Hom.: 27436 Cov.: 31

Gnomad AFR AF: 0.428

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.705

Gnomad EAS AF: 0.714

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.628

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.623

GnomAD4 exome AF: 0.640 AC: 6199 AN: 9684 Hom.: 2077 Cov.: 0 AF XY: 0.632 AC XY: 3181 AN XY: 5030

Gnomad4 AFR exome AF: 0.417

Gnomad4 AMR exome AF: 0.650

Gnomad4 ASJ exome AF: 0.716

Gnomad4 EAS exome AF: 0.805

Gnomad4 SAS exome AF: 0.561

Gnomad4 FIN exome AF: 0.654

Gnomad4 NFE exome AF: 0.646

Gnomad4 OTH exome AF: 0.631

GnomAD4 genome AF: 0.592 AC: 89984 AN: 152036 Hom.: 27456 Cov.: 31 AF XY: 0.593 AC XY: 44073 AN XY: 74324

Gnomad4 AFR AF: 0.428

Gnomad4 AMR AF: 0.658

Gnomad4 ASJ AF: 0.705

Gnomad4 EAS AF: 0.714

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.628

Gnomad4 NFE AF: 0.656

Gnomad4 OTH AF: 0.624

Alfa AF: 0.645 Hom.: 41944

Bravo AF: 0.586

Asia WGS AF: 0.659 AC: 2291 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	0.67
DANN	Benign	0.56

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: rs2110597; hg19: chr12-12941013;