Genetic Variant PINX1-DT:n.301-275G>A (chr8-10845943-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 ENST00000522026.3(PINX1-DT):n.301-275G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,930 control chromosomes in the GnomAD database, including 11,175 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 0.37 ( 11175 hom., cov: 32)

Consequence

PINX1-DT
ENST00000522026.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.254

Publications

8 publications found

Variant links:

Genes affected

PINX1-DT (HGNC:55532): (PINX1 divergent transcript)

PINX1-DT 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=-0.96).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PINX1-DT	NR_125432.1 link	n.154-275G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
PINX1-DT	ENST00000522026.3 link	n.301-275G>A	intron_variant	Intron 3 of 3	3
PINX1-DT	ENST00000655622.2 link	n.239-275G>A	intron_variant	Intron 2 of 2
PINX1-DT	ENST00000821831.1 link	n.161-275G>A	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.365

AC:

55441

AN:

151812

Hom.:

11163

Cov.:

show subpopulations

Gnomad AFR

AF:

0.533

Gnomad AMI

AF:

0.188

Gnomad AMR

AF:

0.273

Gnomad ASJ

AF:

0.398

Gnomad EAS

AF:

0.221

Gnomad SAS

AF:

0.239

Gnomad FIN

AF:

0.276

Gnomad MID

AF:

0.418

Gnomad NFE

AF:

0.318

Gnomad OTH

AF:

0.367

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

GnomAD4 genome

AF:

0.365

AC:

55487

AN:

151930

Hom.:

11175

Cov.:

AF XY:

0.359

AC XY:

26646

AN XY:

74266

show subpopulations

African (AFR)

AF:

0.533

AC:

22071

AN:

41416

American (AMR)

AF:

0.273

AC:

4163

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.398

AC:

1381

AN:

3468

East Asian (EAS)

AF:

0.221

AC:

1138

AN:

5158

South Asian (SAS)

AF:

0.240

AC:

1158

AN:

4816

European-Finnish (FIN)

AF:

0.276

AC:

2913

AN:

10546

Middle Eastern (MID)

AF:

0.418

AC:

123

AN:

294

European-Non Finnish (NFE)

AF:

0.318

AC:

21588

AN:

67936

Other (OTH)

AF:

0.370

AC:

781

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1692

3384

5075

6767

8459

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

518

1036

1554

2072

2590

<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:

0.322

Hom.:

1483

Bravo

AF:

0.372

Asia WGS

AF:

0.240

AC:

835

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.96

CADD

Benign

1.1

(source)

DANN

Benign

0.36

PhyloP100

-0.25

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