ENST00000577647.2:n.*1276C>T

Variant names:

• chr17-63510765-C-T
• rs7221780
• ENST00000577647.2:n.*1276C>T

Variant summary

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

The ENST00000577647.2(ENSG00000264813):​n.*1276C>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: ENSG00000264813 ENST00000577647.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 6.28
• Publications: 6 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=-0.51).
• 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 rank	MANE	Protein	UniProt
ACE3P		n.63510765C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264813	ENST00000577647.2	n.*1276C>T		non_coding_transcript_exon_variant	Exon 24 of 31	2		ENSP00000464149.1
ENSG00000264813	ENST00000577647.2	n.*1276C>T		3_prime_UTR_variant	Exon 24 of 31	2		ENSP00000464149.1
ACE3P	ENST00000423435.2	n.1221C>T		non_coding_transcript_exon_variant	Exon 9 of 13	6

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.491 AC: 210 AN: 428

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.417 AC: 10 AN: 24

Other (OTH) AF: 0.333 AC: 2 AN: 6

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

African (AFR) AF: 0.768 AC: 31657 AN: 41244

American (AMR) AF: 0.491 AC: 7471 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2292 AN: 3460

East Asian (EAS) AF: 0.251 AC: 1295 AN: 5152

South Asian (SAS) AF: 0.404 AC: 1939 AN: 4802

European-Finnish (FIN) AF: 0.471 AC: 4936 AN: 10480

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.573 AC: 38843 AN: 67786

Other (OTH) AF: 0.613 AC: 1293 AN: 2110

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
PhyloP100		6.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7221780; hg19: chr17-61588126;