rs752590

Variant names:

• chr2-113215368-A-G
• rs752590
• ENST00000456685.5:n.99-788A>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 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
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PAX8-AS1	ENST00000456685.5	n.99-788A>G		intron_variant	Intron 1 of 5	1
PAX8-AS1	ENST00000662215.1	n.199+3749A>G		intron_variant	Intron 1 of 3

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;