rs2110597

Variant names:

• chr12-12788079-G-A
• rs2110597
• NM_030817.3:c.*427G>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.*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
• 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]

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
APOLD1	NM_030817.3	c.*427G>A		3_prime_UTR_variant	Exon 2 of 2	ENST00000356591.5	NP_110444.3
APOLD1	NM_001130415.2	c.*427G>A		3_prime_UTR_variant	Exon 2 of 2		NP_001123887.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
APOLD1	ENST00000356591.5	c.*427G>A		3_prime_UTR_variant	Exon 2 of 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

African (AFR) AF: 0.417 AC: 70 AN: 168

American (AMR) AF: 0.650 AC: 688 AN: 1058

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 149 AN: 208

East Asian (EAS) AF: 0.805 AC: 177 AN: 220

South Asian (SAS) AF: 0.561 AC: 435 AN: 776

European-Finnish (FIN) AF: 0.654 AC: 161 AN: 246

Middle Eastern (MID) AF: 0.542 AC: 13 AN: 24

European-Non Finnish (NFE) AF: 0.646 AC: 4193 AN: 6488

Other (OTH) AF: 0.631 AC: 313 AN: 496

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

African (AFR) AF: 0.428 AC: 17723 AN: 41444

American (AMR) AF: 0.658 AC: 10052 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.705 AC: 2448 AN: 3470

East Asian (EAS) AF: 0.714 AC: 3692 AN: 5168

South Asian (SAS) AF: 0.563 AC: 2711 AN: 4818

European-Finnish (FIN) AF: 0.628 AC: 6633 AN: 10554

Middle Eastern (MID) AF: 0.711 AC: 209 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44635 AN: 67992

Other (OTH) AF: 0.624 AC: 1316 AN: 2108

Alfa AF: 0.639 Hom.: 52452

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
PhyloP100		-0.62
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: rs2110597; hg19: chr12-12941013;