rs2863244

Variant names:

• chr2-113243289-A-G
• rs2863244
• NM_003466.4:c.390-511T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003466.4(PAX8):​c.390-511T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,090 control chromosomes in the GnomAD database, including 18,524 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 0.49 (18524 hom., cov: 33)
• Consequence: PAX8 NM_003466.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.181
• Publications: 16 publications found

Genes affected

PAX8 (HGNC:8622): (paired box 8) This gene encodes a member of the paired box (PAX) family of transcription factors. Members of this gene family typically encode proteins that contain a paired box domain, an octapeptide, and a paired-type homeodomain. This nuclear protein is involved in thyroid follicular cell development and expression of thyroid-specific genes. Mutations in this gene have been associated with thyroid dysgenesis, thyroid follicular carcinomas and atypical follicular thyroid adenomas. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Mar 2010]

PAX8-AS1 (HGNC:49271): (PAX8 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.584 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003466.4. 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
	PAX8	NM_003466.4	MANE Select	c.390-511T>C		intron	N/A	NP_003457.1
	PAX8	NM_013952.4		c.390-511T>C		intron	N/A	NP_039246.1
	PAX8	NM_013953.4		c.390-511T>C		intron	N/A	NP_039247.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX8	ENST00000429538.8	TSL:1 MANE Select	c.390-511T>C		intron	N/A	ENSP00000395498.3
	PAX8	ENST00000263334.9	TSL:1	c.390-511T>C		intron	N/A	ENSP00000263334.6
	PAX8	ENST00000348715.9	TSL:1	c.390-511T>C		intron	N/A	ENSP00000314750.5

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74112 AN: 151970 Hom.: 18506 Cov.: 33

Gnomad AFR AF: 0.590

Gnomad AMI AF: 0.617

Gnomad AMR AF: 0.432

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.489

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.466

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

GnomAD4 genome AF: 0.488 AC: 74189 AN: 152090 Hom.: 18524 Cov.: 33 AF XY: 0.490 AC XY: 36467 AN XY: 74354

African (AFR) AF: 0.590 AC: 24487 AN: 41494

American (AMR) AF: 0.432 AC: 6611 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1509 AN: 3466

East Asian (EAS) AF: 0.310 AC: 1607 AN: 5176

South Asian (SAS) AF: 0.488 AC: 2354 AN: 4822

European-Finnish (FIN) AF: 0.539 AC: 5701 AN: 10572

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30274 AN: 67948

Other (OTH) AF: 0.466 AC: 984 AN: 2112

Alfa AF: 0.453 Hom.: 26741

Bravo AF: 0.481

Asia WGS AF: 0.473 AC: 1644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.55
DANN	Benign	0.51
PhyloP100		-0.18
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: rs2863244; hg19: chr2-114000866;