rs485874

Positions:

• chr1-18746432-A-G
• chr1-18746432-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001135254.2(PAX7):​c.*1503A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 230,294 control chromosomes in the GnomAD database, including 38,556 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 0.58 (26234 hom., cov: 31)
  • Exomes 𝑓: 0.56 (12322 hom.)
• Consequence: PAX7 NM_001135254.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.394

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.683 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX7	NM_001135254.2	c.*1503A>G		3_prime_UTR_variant	9/9	ENST00000420770.7	NP_001128726.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAX7	ENST00000420770.7	c.*1503A>G		3_prime_UTR_variant	9/9	1	NM_001135254.2	ENSP00000403389	P1

Frequencies

GnomAD3 genomes AF: 0.582 AC: 88449 AN: 151866 Hom.: 26218 Cov.: 31

Gnomad AFR AF: 0.690

Gnomad AMI AF: 0.546

Gnomad AMR AF: 0.513

Gnomad ASJ AF: 0.666

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.618

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.685

Gnomad NFE AF: 0.552

Gnomad OTH AF: 0.594

GnomAD4 exome AF: 0.557 AC: 43635 AN: 78308 Hom.: 12322 Cov.: 0 AF XY: 0.561 AC XY: 20248 AN XY: 36064

Gnomad4 AFR exome AF: 0.693

Gnomad4 AMR exome AF: 0.493

Gnomad4 ASJ exome AF: 0.670

Gnomad4 EAS exome AF: 0.450

Gnomad4 SAS exome AF: 0.652

Gnomad4 FIN exome AF: 0.463

Gnomad4 NFE exome AF: 0.560

Gnomad4 OTH exome AF: 0.568

GnomAD4 genome AF: 0.582 AC: 88506 AN: 151986 Hom.: 26234 Cov.: 31 AF XY: 0.576 AC XY: 42751 AN XY: 74266

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.666

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.618

Gnomad4 FIN AF: 0.466

Gnomad4 NFE AF: 0.552

Gnomad4 OTH AF: 0.593

Alfa AF: 0.555 Hom.: 30841

Bravo AF: 0.589

Asia WGS AF: 0.558 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.64

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

Other links and lift over

dbSNP: rs485874; hg19: chr1-19072926;