chr7-127610587-G-GCATA

Position:

• chr7-127610587-G-GCATA

Variant summary

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

The NM_001366110.1(PAX4):​c.*476_*477insTATG variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.44 (15755 hom., cov: 0)
  • Exomes 𝑓: 0.39 (23715 hom.)
• Consequence: PAX4 NM_001366110.1 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.505

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 7-127610587-G-GCATA is Benign according to our data. Variant chr7-127610587-G-GCATA is described in ClinVar as [Benign]. Clinvar id is 358788.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.596 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAX4	NM_001366110.1	c.*476_*477insTATG		3_prime_UTR_variant	12/12	ENST00000639438.3
PAX4	NM_001366111.1	c.*264_*265insTATG		3_prime_UTR_variant	10/10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAX4	ENST00000639438.3	c.*476_*477insTATG		3_prime_UTR_variant	12/12	5	NM_001366110.1	A2
PAX4	ENST00000341640.6	c.*476_*477insTATG		3_prime_UTR_variant	9/9	1

Frequencies

GnomAD3 genomes AF: 0.442 AC: 67118 AN: 151724 Hom.: 15730 Cov.: 0

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.381

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.397

Gnomad EAS AF: 0.266

Gnomad SAS AF: 0.440

Gnomad FIN AF: 0.424

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.415

GnomAD4 exome AF: 0.386 AC: 111876 AN: 290072 Hom.: 23715 Cov.: 0 AF XY: 0.387 AC XY: 59274 AN XY: 153284

Gnomad4 AFR exome AF: 0.589

Gnomad4 AMR exome AF: 0.301

Gnomad4 ASJ exome AF: 0.379

Gnomad4 EAS exome AF: 0.235

Gnomad4 SAS exome AF: 0.431

Gnomad4 FIN exome AF: 0.432

Gnomad4 NFE exome AF: 0.382

Gnomad4 OTH exome AF: 0.393

GnomAD4 genome AF: 0.442 AC: 67174 AN: 151842 Hom.: 15755 Cov.: 0 AF XY: 0.440 AC XY: 32665 AN XY: 74198

Gnomad4 AFR AF: 0.602

Gnomad4 AMR AF: 0.354

Gnomad4 ASJ AF: 0.397

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.438

Gnomad4 FIN AF: 0.424

Gnomad4 NFE AF: 0.386

Gnomad4 OTH AF: 0.410

Alfa AF: 0.417 Hom.: 1087

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Maturity onset diabetes mellitus in young Benign:1

Benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

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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: rs66998513; hg19: chr7-127250641;