rs7221780

Positions:

• chr17-63510765-C-T

Variant summary

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

The ENST00000423435.2(ACE3P):​n.1221C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.598 in 151,920 control chromosomes in the GnomAD database, including 28,388 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 0.60 (28337 hom., cov: 31)
  • Exomes 𝑓: 0.48 (51 hom.)
• Consequence: ACE3P ENST00000423435.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.28

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=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.76 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.1221C>T		non_coding_transcript_exon_variant	9/13

Frequencies

GnomAD3 genomes AF: 0.598 AC: 90493 AN: 151346 Hom.: 28298 Cov.: 31

Gnomad AFR AF: 0.767

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.491

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.252

Gnomad SAS AF: 0.404

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.758

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.616

GnomAD4 exome AF: 0.485 AC: 222 AN: 458 Hom.: 51 Cov.: 0 AF XY: 0.482 AC XY: 133 AN XY: 276

Gnomad4 FIN exome AF: 0.491

Gnomad4 NFE exome AF: 0.417

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.598 AC: 90578 AN: 151462 Hom.: 28337 Cov.: 31 AF XY: 0.586 AC XY: 43352 AN XY: 73976

Gnomad4 AFR AF: 0.768

Gnomad4 AMR AF: 0.491

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.404

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.613

Alfa AF: 0.620 Hom.: 4873

Bravo AF: 0.608

Asia WGS AF: 0.346 AC: 1209 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		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: rs7221780; hg19: chr17-61588126;