rs485874

Variant names:

• chr1-18746432-A-G
• rs485874
• NM_001135254.2:c.*1503A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

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 Gene-Disease associations (from GenCC):

• myopathy, congenital, progressive, with scoliosis

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), Illumina
• congenital myopathy with myasthenic-like onset

  Inheritance: AR Classification: MODERATE Submitted by: ClinGen

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001135254.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX7	NM_001135254.2	MANE Select	c.*1503A>G		3_prime_UTR	Exon 9 of 9	NP_001128726.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX7	ENST00000420770.7	TSL:1 MANE Select	c.*1503A>G		3_prime_UTR	Exon 9 of 9	ENSP00000403389.2
	PAX7	ENST00000713641.1		n.*1813A>G		non_coding_transcript_exon	Exon 10 of 10	ENSP00000518942.1
	PAX7	ENST00000713640.1		c.*1503A>G		3_prime_UTR	Exon 10 of 10	ENSP00000518941.1

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

African (AFR) AF: 0.693 AC: 2604 AN: 3758

American (AMR) AF: 0.493 AC: 1189 AN: 2410

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 3327 AN: 4964

East Asian (EAS) AF: 0.450 AC: 4985 AN: 11066

South Asian (SAS) AF: 0.652 AC: 438 AN: 672

European-Finnish (FIN) AF: 0.463 AC: 25 AN: 54

Middle Eastern (MID) AF: 0.603 AC: 288 AN: 478

European-Non Finnish (NFE) AF: 0.560 AC: 27063 AN: 48358

Other (OTH) AF: 0.568 AC: 3716 AN: 6548

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

African (AFR) AF: 0.689 AC: 28591 AN: 41468

American (AMR) AF: 0.512 AC: 7810 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.666 AC: 2310 AN: 3470

East Asian (EAS) AF: 0.479 AC: 2474 AN: 5170

South Asian (SAS) AF: 0.618 AC: 2970 AN: 4804

European-Finnish (FIN) AF: 0.466 AC: 4922 AN: 10554

Middle Eastern (MID) AF: 0.697 AC: 205 AN: 294

European-Non Finnish (NFE) AF: 0.552 AC: 37479 AN: 67946

Other (OTH) AF: 0.593 AC: 1249 AN: 2106

Alfa AF: 0.559 Hom.: 39977

Bravo AF: 0.589

Asia WGS AF: 0.558 AC: 1944 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.81
DANN	Benign	0.64
PhyloP100		-0.39
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs485874; hg19: chr1-19072926;