Variant chr1-18703052-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001135254.2(PAX7):c.953-42A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.302 in 1,570,530 control chromosomes in the GnomAD database, including 80,130 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 0.39 ( 12878 hom., cov: 33)

Exomes 𝑓: 0.29 ( 67252 hom. )

Consequence

PAX7
NM_001135254.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.419

Variant links:

Genes affected

PAX7 (HGNC:8621): (paired box 7) This gene is a member of the paired box (PAX) family of transcription factors. Members of this gene family typically contain a paired box domain, an octapeptide, and a paired-type homeodomain. These genes play critical roles during fetal development and cancer growth. The specific function of the paired box 7 gene is unknown but speculated to involve tumor suppression since fusion of this gene with a forkhead domain family member has been associated with alveolar rhabdomyosarcoma. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2008]

PAX7 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein	UniProt
PAX7	NM_001135254.2 link	c.953-42A>G	intron_variant	ENST00000420770.7	NP_001128726.1	P23759-3
PAX7	NM_002584.3 link	c.953-42A>G	intron_variant		NP_002575.1	P23759-1
PAX7	NM_013945.3 link	c.947-42A>G	intron_variant		NP_039236.1	P23759-2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
PAX7	ENST00000420770.7 link	c.953-42A>G	intron_variant	1	NM_001135254.2	ENSP00000403389.2	P23759-3
PAX7	ENST00000375375.7 link	c.953-42A>G	intron_variant	1		ENSP00000364524.3	P23759-1
PAX7	ENST00000400661.3 link	c.947-42A>G	intron_variant	1		ENSP00000383502.3	P23759-2

Frequencies

GnomAD3 genomes

AF:

0.386

AC:

58585

AN:

151910

Hom.:

12853

Cov.:

show subpopulations

Gnomad AFR

AF:

0.588

Gnomad AMI

AF:

0.367

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.395

Gnomad EAS

AF:

0.602

Gnomad SAS

AF:

0.405

Gnomad FIN

AF:

0.315

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.258

Gnomad OTH

AF:

0.374

GnomAD3 exomes

AF:

0.370

AC:

89162

AN:

241200

Hom.:

18175

AF XY:

0.361

AC XY:

47494

AN XY:

131462

show subpopulations

Gnomad AFR exome

AF:

0.594

Gnomad AMR exome

AF:

0.467

Gnomad ASJ exome

AF:

0.394

Gnomad EAS exome

AF:

0.603

Gnomad SAS exome

AF:

0.401

Gnomad FIN exome

AF:

0.323

Gnomad NFE exome

AF:

0.267

Gnomad OTH exome

AF:

0.334

GnomAD4 exome

AF:

0.293

AC:

416227

AN:

1418502

Hom.:

67252

Cov.:

AF XY:

0.295

AC XY:

207783

AN XY:

703646

show subpopulations

Gnomad4 AFR exome

AF:

0.598

Gnomad4 AMR exome

AF:

0.454

Gnomad4 ASJ exome

AF:

0.392

Gnomad4 EAS exome

AF:

0.584

Gnomad4 SAS exome

AF:

0.396

Gnomad4 FIN exome

AF:

0.325

Gnomad4 NFE exome

AF:

0.253

Gnomad4 OTH exome

AF:

0.328

GnomAD4 genome

AF:

0.386

AC:

58661

AN:

152028

Hom.:

12878

Cov.:

AF XY:

0.386

AC XY:

28687

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.588

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.395

Gnomad4 EAS

AF:

0.601

Gnomad4 SAS

AF:

0.404

Gnomad4 FIN

AF:

0.315

Gnomad4 NFE

AF:

0.258

Gnomad4 OTH

AF:

0.376

Alfa

AF:

0.325

Hom.:

2384

Bravo

AF:

0.403

Asia WGS

AF:

0.507

AC:

1763

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

DANN

Benign

0.53

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over