17-63511904-T-C

Variant names:

• chr17-63511904-T-C
• rs8066276
• ENST00000577647.2:n.*1343+1072T>C

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.*1343+1072T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.497 in 152,122 control chromosomes in the GnomAD database, including 19,949 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 (19949 hom., cov: 32)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 23 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=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.601 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACE3P		n.63511904T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264813	ENST00000577647.2	n.*1343+1072T>C		intron_variant	Intron 24 of 30	2		ENSP00000464149.1
ACE3P	ENST00000423435.2	n.1288+1072T>C		intron_variant	Intron 9 of 12	6

Frequencies

GnomAD3 genomes AF: 0.497 AC: 75522 AN: 152004 Hom.: 19949 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.709

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.685

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.561

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

GnomAD4 genome AF: 0.497 AC: 75537 AN: 152122 Hom.: 19949 Cov.: 32 AF XY: 0.487 AC XY: 36232 AN XY: 74364

African (AFR) AF: 0.345 AC: 14297 AN: 41494

American (AMR) AF: 0.471 AC: 7202 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.685 AC: 2375 AN: 3468

East Asian (EAS) AF: 0.257 AC: 1326 AN: 5158

South Asian (SAS) AF: 0.403 AC: 1947 AN: 4830

European-Finnish (FIN) AF: 0.485 AC: 5134 AN: 10584

Middle Eastern (MID) AF: 0.762 AC: 224 AN: 294

European-Non Finnish (NFE) AF: 0.606 AC: 41208 AN: 67972

Other (OTH) AF: 0.557 AC: 1177 AN: 2112

Alfa AF: 0.575 Hom.: 40288

Bravo AF: 0.488

Asia WGS AF: 0.310 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.46
PhyloP100		-0.77
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs8066276; hg19: chr17-61589265;