rs7221780

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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000264813	ENST00000577647.2	TSL:2	n.*1276C>T		non_coding_transcript_exon	Exon 24 of 31	ENSP00000464149.1	F6X3S4
	ENSG00000264813	ENST00000577647.2	TSL:2	n.*1276C>T		3_prime_UTR	Exon 24 of 31	ENSP00000464149.1	F6X3S4
	ACE3P	ENST00000423435.2		n.1221C>T		non_coding_transcript_exon	Exon 9 of 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

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 v4.9

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;