chr7-127610570-T-TGC

Position:

• chr7-127610570-T-TGC

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_001366110.1(PAX4):​c.*493_*494insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.23 (3019 hom., cov: 18)
  • Exomes 𝑓: 0.14 (2427 hom.)
• Consequence: PAX4 NM_001366110.1 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.415

Genes affected

PAX4 (HGNC:8618): (paired box 4) 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 paired box 4 gene is involved in pancreatic islet development and mouse studies have demonstrated a role for this gene in differentiation of insulin-producing beta cells. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 7-127610570-T-TGC is Benign according to our data. Variant chr7-127610570-T-TGC is described in ClinVar as [Likely_benign]. Clinvar id is 358782.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.31 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAX4	NM_001366110.1	c.*493_*494insGC		3_prime_UTR_variant	12/12	ENST00000639438.3
PAX4	NM_001366111.1	c.*281_*282insGC		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAX4	ENST00000639438.3	c.*493_*494insGC		3_prime_UTR_variant	12/12	5	NM_001366110.1	A2
PAX4	ENST00000341640.6	c.*493_*494insGC		3_prime_UTR_variant	9/9	1

Frequencies

GnomAD3 genomes AF: 0.229 AC: 30112 AN: 131484 Hom.: 3017 Cov.: 18

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.172

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.228

GnomAD4 exome AF: 0.145 AC: 26332 AN: 181612 Hom.: 2427 Cov.: 0 AF XY: 0.149 AC XY: 14324 AN XY: 96050

Gnomad4 AFR exome AF: 0.163

Gnomad4 AMR exome AF: 0.103

Gnomad4 ASJ exome AF: 0.106

Gnomad4 EAS exome AF: 0.0759

Gnomad4 SAS exome AF: 0.204

Gnomad4 FIN exome AF: 0.130

Gnomad4 NFE exome AF: 0.146

Gnomad4 OTH exome AF: 0.135

GnomAD4 genome AF: 0.229 AC: 30127 AN: 131580 Hom.: 3019 Cov.: 18 AF XY: 0.228 AC XY: 14653 AN XY: 64218

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.325

Gnomad4 FIN AF: 0.208

Gnomad4 NFE AF: 0.251

Gnomad4 OTH AF: 0.227

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Maturity onset diabetes mellitus in young Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs61297182; hg19: chr7-127250624;