ENST00000577647.2:n.*1344-903C>G

Variant names:

• chr17-63512479-C-G
• rs8066114
• ENST00000577647.2:n.*1344-903C>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577647.2(ENSG00000264813):​n.*1344-903C>G variant causes a intron 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: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.735
• Publications: 17 publications found

Genes affected

ENSG00000264813 (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577647.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264813	ENST00000577647.2	TSL:2	n.*1344-903C>G		intron	N/A	ENSP00000464149.1
	ACE3P	ENST00000423435.2	TSL:6	n.1289-903C>G		intron	N/A

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

African (AFR) AF: 0.279 AC: 11527 AN: 41348

American (AMR) AF: 0.341 AC: 5208 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1670 AN: 3472

East Asian (EAS) AF: 0.217 AC: 1120 AN: 5162

South Asian (SAS) AF: 0.310 AC: 1490 AN: 4806

European-Finnish (FIN) AF: 0.364 AC: 3835 AN: 10546

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.405 AC: 27524 AN: 67924

Other (OTH) AF: 0.377 AC: 795 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.57
DANN	Benign	0.75
PhyloP100		-0.73
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: rs8066114; hg19: chr17-61589840;