rs752590

chr2-113215368-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000456685.5(PAX8-AS1):n.99-788A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 151,986 control chromosomes in the GnomAD database, including 5,933 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 0.26 (5933 hom., cov: 32)
• Consequence: PAX8-AS1 ENST00000456685.5 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.966

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAX8-AS1	ENST00000456685.5	n.99-788A>G		intron_variant, non_coding_transcript_variant		1
PAX8-AS1	ENST00000662215.1	n.199+3749A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40029 AN: 151868 Hom.: 5915 Cov.: 32

Gnomad AFR AF: 0.411

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.159

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.275

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.264 AC: 40092 AN: 151986 Hom.: 5933 Cov.: 32 AF XY: 0.262 AC XY: 19462 AN XY: 74298

Gnomad4 AFR AF: 0.411

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.159

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.275

Gnomad4 NFE AF: 0.212

Gnomad4 OTH AF: 0.214

Alfa AF: 0.217 Hom.: 2278

Bravo AF: 0.263

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	2.2
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs752590; hg19: chr2-113972945;