14-36657666-A-AC

Variant summary

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

The ENST00000555107.1(ENSG00000258661):n.258+877_258+878insG variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.39 (11494 hom., cov: 0)
  • Exomes 𝑓: 0.31 (1 hom.)
• Consequence: ENST00000555107.1 intron, non_coding_transcript
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.683

Genes affected

(HGNC:):

PAX9 (HGNC:8623): (paired box 9) 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. Mice lacking this gene exhibit impaired development of organs, musculature and the skeleton, including absent and abnormally developed teeth, and neonatal lethality. Mutations in the human gene are associated with selective tooth agenesis-3. [provided by RefSeq, Sep 2015]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 14-36657666-A-AC is Benign according to our data. Variant chr14-36657666-A-AC is described in ClinVar as [Likely_benign]. Clinvar id is 313152.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105370455	XR_943758.3	n.206+877_206+878insG		intron_variant, non_coding_transcript_variant
PAX9	NM_006194.4	c.-626dup		5_prime_UTR_variant	1/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000555107.1	n.258+877_258+878insG		intron_variant, non_coding_transcript_variant		3
PAX9	ENST00000402703.6	c.-626dup		5_prime_UTR_variant	1/5	5		P1
PAX9	ENST00000553267.4	n.101dup		non_coding_transcript_exon_variant	1/2	4
PAX9	ENST00000555639.2			upstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58632 AN: 151880 Hom.: 11475 Cov.: 0

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.405

GnomAD4 exome AF: 0.308 AC: 8 AN: 26 Hom.: 1 Cov.: 0 AF XY: 0.364 AC XY: 8 AN XY: 22

Gnomad4 NFE exome AF: 0.364

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.386 AC: 58695 AN: 151998 Hom.: 11494 Cov.: 0 AF XY: 0.385 AC XY: 28613 AN XY: 74278

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.431

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.404

Alfa AF: 0.368 Hom.: 1234

Bravo AF: 0.388

Asia WGS AF: 0.415 AC: 1447 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Selective tooth agenesis Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Illumina Laboratory Services, Illumina

Jun 14, 2016

- -

Computational scores

Source: dbNSFP v4.3

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: rs397830943; hg19: chr14-37126871;