dbSNP rs477687: PITX1-AS1:n.281-42032G>A (chr5-135132010-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

The ENST00000505828.5(PITX1-AS1):n.281-42032G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,192 control chromosomes in the GnomAD database, including 2,702 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 0.18 ( 2702 hom., cov: 33)

Consequence

PITX1-AS1
ENST00000505828.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.03

Publications

11 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 -10 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.29).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1 link	n.337-42032G>A		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PITX1-AS1	ENST00000505828.5 link	n.281-42032G>A	intron_variant	Intron 3 of 4	4
PITX1-AS1	ENST00000507058.1 link	n.47-1217G>A	intron_variant	Intron 1 of 2	3
PITX1-AS1	ENST00000507641.5 link	n.430-15073G>A	intron_variant	Intron 4 of 4	3

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27483

AN:

152074

Hom.:

2695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.115

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.00520

Gnomad SAS

AF:

0.0942

Gnomad FIN

AF:

0.158

Gnomad MID

AF:

0.185

Gnomad NFE

AF:

0.174

Gnomad OTH

AF:

0.176

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

GnomAD4 genome

AF:

0.181

AC:

27505

AN:

152192

Hom.:

2702

Cov.:

AF XY:

0.180

AC XY:

13367

AN XY:

74404

show subpopulations

African (AFR)

AF:

0.251

AC:

10437

AN:

41512

American (AMR)

AF:

0.133

AC:

2033

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.154

AC:

533

AN:

3466

East Asian (EAS)

AF:

0.00521

AC:

AN:

5180

South Asian (SAS)

AF:

0.0947

AC:

457

AN:

4824

European-Finnish (FIN)

AF:

0.158

AC:

1676

AN:

10600

Middle Eastern (MID)

AF:

0.192

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.174

AC:

11813

AN:

67992

Other (OTH)

AF:

0.174

AC:

368

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1165

2330

3494

4659

5824

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.173

Hom.:

8879

Bravo

AF:

0.182

Asia WGS

AF:

0.0650

AC:

225

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.29

CADD

Benign

(source)

DANN

Benign

0.72

PhyloP100

2.0

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