Genetic Variant ENSG00000264813:n.2145A>T (chr17-63507359-A-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000577647.2(ENSG00000264813):n.2145A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.54 in 398,798 control chromosomes in the GnomAD database, including 60,001 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 0.54 ( 22985 hom., cov: 32)

Exomes 𝑓: 0.54 ( 37016 hom. )

Consequence

ENSG00000264813
ENST00000577647.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.117

Publications

19 publications found

Variant links:

Genes affected

ENSG00000264813 (HGNC:):

ENSG00000264813 links:

ACE3P (HGNC:44365): (angiotensin I converting enzyme 3, pseudogene) Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACE3P links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.57 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ACE3P		n.63507359A>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000264813	ENST00000577647.2 link	n.2145A>T		non_coding_transcript_exon_variant	Exon 15 of 31	2		ENSP00000464149.1		F6X3S4
ACE3P	ENST00000423435.2 link	n.58-205A>T		intron_variant	Intron 1 of 12	6

Frequencies

GnomAD3 genomes

AF:

0.544

AC:

82666

AN:

151888

Hom.:

22965

Cov.:

show subpopulations

Gnomad AFR

AF:

0.575

Gnomad AMI

AF:

0.698

Gnomad AMR

AF:

0.473

Gnomad ASJ

AF:

0.663

Gnomad EAS

AF:

0.259

Gnomad SAS

AF:

0.404

Gnomad FIN

AF:

0.474

Gnomad MID

AF:

0.734

Gnomad NFE

AF:

0.574

Gnomad OTH

AF:

0.580

GnomAD2 exomes

AF:

0.552

AC:

4845

AN:

8782

AF XY:

0.559

show subpopulations

Gnomad AFR exome

AF:

0.535

Gnomad AMR exome

AF:

0.424

Gnomad ASJ exome

AF:

0.707

Gnomad EAS exome

AF:

0.236

Gnomad FIN exome

AF:

0.486

Gnomad NFE exome

AF:

0.572

Gnomad OTH exome

AF:

0.592

GnomAD4 exome

AF:

0.537

AC:

132457

AN:

246792

Hom.:

37016

Cov.:

AF XY:

0.541

AC XY:

67622

AN XY:

125090

show subpopulations

African (AFR)

AF:

0.581

AC:

4175

AN:

7180

American (AMR)

AF:

0.437

AC:

3252

AN:

7434

Ashkenazi Jewish (ASJ)

AF:

0.680

AC:

6286

AN:

9240

East Asian (EAS)

AF:

0.267

AC:

6109

AN:

22894

South Asian (SAS)

AF:

0.404

AC:

1226

AN:

3032

European-Finnish (FIN)

AF:

0.496

AC:

10542

AN:

21260

Middle Eastern (MID)

AF:

0.685

AC:

887

AN:

1294

European-Non Finnish (NFE)

AF:

0.576

AC:

91108

AN:

158074

Other (OTH)

AF:

0.542

AC:

8872

AN:

16384

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

3772

7544

11316

15088

18860

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

342

684

1026

1368

1710

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.544

AC:

82721

AN:

152006

Hom.:

22985

Cov.:

AF XY:

0.534

AC XY:

39639

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.575

AC:

23831

AN:

41480

American (AMR)

AF:

0.472

AC:

7212

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.663

AC:

2302

AN:

3470

East Asian (EAS)

AF:

0.259

AC:

1334

AN:

5156

South Asian (SAS)

AF:

0.405

AC:

1948

AN:

4814

European-Finnish (FIN)

AF:

0.474

AC:

5007

AN:

10572

Middle Eastern (MID)

AF:

0.738

AC:

217

AN:

294

European-Non Finnish (NFE)

AF:

0.574

AC:

39024

AN:

67936

Other (OTH)

AF:

0.576

AC:

1214

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1934

3868

5803

7737

9671

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

708

1416

2124

2832

3540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.566

Hom.:

3047

Bravo

AF:

0.544

Asia WGS

AF:

0.331

AC:

1157

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

9.0

(source)

DANN

Benign

0.75

PhyloP100

-0.12

Mutation Taster

=98/2

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over