rs4611524

Variant names:

• chr17-63514291-T-C
• rs4611524
• ENST00000577647.2:n.*1549+197T>C

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.*1549+197T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,040 control chromosomes in the GnomAD database, including 22,137 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 0.53 (22137 hom., cov: 32)
• Consequence: ENSG00000264813 ENST00000577647.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.372
• Publications: 12 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=-0.67).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.593 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACE3P		n.63514291T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264813	ENST00000577647.2	n.*1549+197T>C		intron_variant	Intron 26 of 30	2		ENSP00000464149.1
ACE3P	ENST00000423435.2	n.1494+197T>C		intron_variant	Intron 11 of 12	6

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80876 AN: 151922 Hom.: 22132 Cov.: 32

Gnomad AFR AF: 0.479

Gnomad AMI AF: 0.726

Gnomad AMR AF: 0.467

Gnomad ASJ AF: 0.690

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.517

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.573

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

GnomAD4 genome AF: 0.532 AC: 80906 AN: 152040 Hom.: 22137 Cov.: 32 AF XY: 0.523 AC XY: 38848 AN XY: 74334

African (AFR) AF: 0.479 AC: 19864 AN: 41468

American (AMR) AF: 0.467 AC: 7130 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.690 AC: 2395 AN: 3472

East Asian (EAS) AF: 0.257 AC: 1328 AN: 5168

South Asian (SAS) AF: 0.415 AC: 1998 AN: 4810

European-Finnish (FIN) AF: 0.517 AC: 5461 AN: 10572

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40654 AN: 67966

Other (OTH) AF: 0.570 AC: 1201 AN: 2108

Alfa AF: 0.571 Hom.: 96167

Bravo AF: 0.524

Asia WGS AF: 0.322 AC: 1123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	8.6
DANN	Benign	0.87
PhyloP100		-0.37
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: rs4611524; hg19: chr17-61591652;