Genetic Variant PITX1-AS1:n.280+33388G>A (chr5-135107916-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000505828.5(PITX1-AS1):n.280+33388G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.318 in 152,166 control chromosomes in the GnomAD database, including 8,811 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 0.32 ( 8811 hom., cov: 33)

Consequence

PITX1-AS1
ENST00000505828.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.144

Publications

46 publications found

Variant links:

Genes affected

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

PITX1-AS1 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=-0.8).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.402 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1 link	n.336+55394G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PITX1-AS1	ENST00000505828.5 link	n.280+33388G>A	intron_variant	Intron 3 of 4	4
PITX1-AS1	ENST00000507641.5 link	n.429+32528G>A	intron_variant	Intron 4 of 4	3
PITX1-AS1	ENST00000624272.3 link	n.330+55394G>A	intron_variant	Intron 2 of 5	2

Frequencies

GnomAD3 genomes

AF:

0.319

AC:

48429

AN:

152048

Hom.:

8806

Cov.:

show subpopulations

Gnomad AFR

AF:

0.135

Gnomad AMI

AF:

0.264

Gnomad AMR

AF:

0.356

Gnomad ASJ

AF:

0.386

Gnomad EAS

AF:

0.227

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.404

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.406

Gnomad OTH

AF:

0.331

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.318

AC:

48461

AN:

152166

Hom.:

8811

Cov.:

AF XY:

0.318

AC XY:

23666

AN XY:

74370

show subpopulations

African (AFR)

AF:

0.135

AC:

5623

AN:

41552

American (AMR)

AF:

0.357

AC:

5456

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.386

AC:

1339

AN:

3466

East Asian (EAS)

AF:

0.227

AC:

1175

AN:

5184

South Asian (SAS)

AF:

0.404

AC:

1945

AN:

4818

European-Finnish (FIN)

AF:

0.404

AC:

4276

AN:

10576

Middle Eastern (MID)

AF:

0.299

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.406

AC:

27617

AN:

67966

Other (OTH)

AF:

0.332

AC:

701

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1639

3279

4918

6558

8197

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

490

980

1470

1960

2450

<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:

0.376

Hom.:

46741

Bravo

AF:

0.300

Asia WGS

AF:

0.319

AC:

1109

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.80

CADD

Benign

4.7

(source)

DANN

Benign

0.75

PhyloP100

0.14

Splicing

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over