rs8066114

chr17-63512479-C-Gchr17-63512479-C-T

Variant summary

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

The ENST00000423435.2(ACE3P):n.1289-903C>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.354 in 151,826 control chromosomes in the GnomAD database, including 9,821 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 0.35 (9821 hom., cov: 30)
• Consequence: ACE3P ENST00000423435.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735

Genes affected

ACE3P (HGNC:44365): (angiotensin I converting enzyme 3, pseudogene) Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ACE3P	ENST00000423435.2	n.1289-903C>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53778 AN: 151708 Hom.: 9822 Cov.: 30

Gnomad AFR AF: 0.279

Gnomad AMI AF: 0.525

Gnomad AMR AF: 0.342

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.490

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.354 AC: 53788 AN: 151826 Hom.: 9821 Cov.: 30 AF XY: 0.350 AC XY: 26002 AN XY: 74204

Gnomad4 AFR AF: 0.279

Gnomad4 AMR AF: 0.341

Gnomad4 ASJ AF: 0.481

Gnomad4 EAS AF: 0.217

Gnomad4 SAS AF: 0.310

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.377

Alfa AF: 0.259 Hom.: 666

Bravo AF: 0.349

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.57
Dann	Benign	0.75

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: rs8066114; hg19: chr17-61589840;