Genetic Variant ENST00000752018.1:n.166C>T (chr2-37827954-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000752018.1(PIRAT1):n.166C>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 0.103 in 396,140 control chromosomes in the GnomAD database, including 2,569 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 0.12 ( 1436 hom., cov: 34)

Exomes 𝑓: 0.091 ( 1133 hom. )

Consequence

PIRAT1
ENST00000752018.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.355

Publications

6 publications found

Variant links:

Genes affected

PIRAT1 (HGNC:37459): (PU.1 (SPI1) induced regulator of S100A8 and S100A9 alarmin transcription 1)

PIRAT1 links:

CDC42EP3-AS1 (HGNC:56370): (CDC42EP3 antisense RNA 1)

CDC42EP3-AS1 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000752018.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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 = 0.215 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000752018.1. 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
	PIRAT1	NR_110011.1		n.571-76C>T		intron	N/A
	PIRAT1	NR_110012.1		n.393-76C>T		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
PIRAT1	ENST00000752018.1		n.166C>T	non_coding_transcript_exon	Exon 1 of 1
PIRAT1	ENST00000413792.5	TSL:2	n.292-76C>T	intron	N/A
PIRAT1	ENST00000418746.2	TSL:4	n.630-76C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18564

AN:

152146

Hom.:

1431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.219

Gnomad AMI

AF:

0.102

Gnomad AMR

AF:

0.0733

Gnomad ASJ

AF:

0.136

Gnomad EAS

AF:

0.0914

Gnomad SAS

AF:

0.0854

Gnomad FIN

AF:

0.107

Gnomad MID

AF:

0.0633

Gnomad NFE

AF:

0.0815

Gnomad OTH

AF:

0.114

GnomAD4 exome

AF:

0.0911

AC:

22222

AN:

243876

Hom.:

1133

AF XY:

0.0902

AC XY:

11156

AN XY:

123640

show subpopulations

African (AFR)

AF:

0.218

AC:

1551

AN:

7110

American (AMR)

AF:

0.0598

AC:

441

AN:

7370

Ashkenazi Jewish (ASJ)

AF:

0.141

AC:

1297

AN:

9184

East Asian (EAS)

AF:

0.0781

AC:

1781

AN:

22792

South Asian (SAS)

AF:

0.0796

AC:

193

AN:

2426

European-Finnish (FIN)

AF:

0.0999

AC:

2061

AN:

20628

Middle Eastern (MID)

AF:

0.0969

AC:

124

AN:

1280

European-Non Finnish (NFE)

AF:

0.0838

AC:

13148

AN:

156832

Other (OTH)

AF:

0.100

AC:

1626

AN:

16254

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

943

1886

2829

3772

4715

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

160

240

320

400

<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:

0.122

AC:

18604

AN:

152264

Hom.:

1436

Cov.:

AF XY:

0.121

AC XY:

8993

AN XY:

74466

show subpopulations

African (AFR)

AF:

0.219

AC:

9089

AN:

41536

American (AMR)

AF:

0.0731

AC:

1119

AN:

15298

Ashkenazi Jewish (ASJ)

AF:

0.136

AC:

471

AN:

3472

East Asian (EAS)

AF:

0.0918

AC:

476

AN:

5186

South Asian (SAS)

AF:

0.0851

AC:

410

AN:

4820

European-Finnish (FIN)

AF:

0.107

AC:

1139

AN:

10610

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0815

AC:

5545

AN:

68022

Other (OTH)

AF:

0.115

AC:

243

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

835

1670

2505

3340

4175

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

206

412

618

824

1030

<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:

0.0918

Hom.:

928

Bravo

AF:

0.124

Asia WGS

AF:

0.101

AC:

353

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

6.0

(source)

DANN

Benign

0.73

PhyloP100

0.35

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over