14-36660788-C-T

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_006194.4(PAX9):c.-393-909C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,166 control chromosomes in the GnomAD database, including 8,117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.32 (8117 hom., cov: 33)
• Consequence: PAX9 NM_006194.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.281

Genes affected

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 14-36660788-C-T is Benign according to our data. Variant chr14-36660788-C-T is described in ClinVar as [Benign]. Clinvar id is 1247478.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAX9	NM_006194.4	c.-393-909C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAX9	ENST00000402703.6	c.-393-909C>T		intron_variant		5		P1
PAX9	ENST00000555639.2	c.-79-1223C>T		intron_variant		5
PAX9	ENST00000553267.4	n.334-909C>T		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48101 AN: 152048 Hom.: 8111 Cov.: 33

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.452

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.376

Gnomad NFE AF: 0.367

Gnomad OTH AF: 0.350

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.316 AC: 48125 AN: 152166 Hom.: 8117 Cov.: 33 AF XY: 0.317 AC XY: 23598 AN XY: 74388

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.285

Gnomad4 ASJ AF: 0.427

Gnomad4 EAS AF: 0.452

Gnomad4 SAS AF: 0.415

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.367

Gnomad4 OTH AF: 0.349

Alfa AF: 0.358 Hom.: 4606

Bravo AF: 0.308

Asia WGS AF: 0.410 AC: 1429 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.0
Dann	Benign	0.69

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: rs2073246; hg19: chr14-37129993;