rs34322

Positions:

• chr12-12726636-T-C

Variant summary

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

The NM_001130415.2(APOLD1):​c.96+540T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 151,930 control chromosomes in the GnomAD database, including 19,457 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 0.50 (19457 hom., cov: 32)
• Consequence: APOLD1 NM_001130415.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.596

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=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
APOLD1	NM_001130415.2	c.96+540T>C		intron_variant			NP_001123887.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
APOLD1	ENST00000326765.10	c.96+540T>C		intron_variant		1		ENSP00000324277.6
APOLD1	ENST00000534843.1	n.*50+263T>C		intron_variant		2		ENSP00000456719.1
APOLD1	ENST00000540583.5	n.*50+263T>C		intron_variant		4		ENSP00000454511.1
APOLD1	ENST00000588943.1	n.71+540T>C		intron_variant		4

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76222 AN: 151812 Hom.: 19444 Cov.: 32

Gnomad AFR AF: 0.431

Gnomad AMI AF: 0.563

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.488

Gnomad SAS AF: 0.528

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.494

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.484

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.502 AC: 76268 AN: 151930 Hom.: 19457 Cov.: 32 AF XY: 0.503 AC XY: 37351 AN XY: 74236

Gnomad4 AFR AF: 0.430

Gnomad4 AMR AF: 0.468

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.488

Gnomad4 SAS AF: 0.531

Gnomad4 FIN AF: 0.593

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.486

Alfa AF: 0.530 Hom.: 33939

Bravo AF: 0.490

Asia WGS AF: 0.483 AC: 1682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.57
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs34322; hg19: chr12-12879570;