rs752590

Variant names:

• chr2-113215368-A-G
• rs752590
• ENST00000456685.5:n.99-788A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 26 publications found

Genes affected

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000456685.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX8-AS1	ENST00000456685.5	TSL:1	n.99-788A>G		intron	N/A
	PAX8-AS1	ENST00000662215.1		n.199+3749A>G		intron	N/A
	PAX8-AS1	ENST00000777999.1		n.141+3749A>G		intron	N/A

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

African (AFR) AF: 0.411 AC: 16994 AN: 41394

American (AMR) AF: 0.187 AC: 2866 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 573 AN: 3470

East Asian (EAS) AF: 0.159 AC: 824 AN: 5176

South Asian (SAS) AF: 0.144 AC: 695 AN: 4822

European-Finnish (FIN) AF: 0.275 AC: 2903 AN: 10568

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.212 AC: 14441 AN: 67960

Other (OTH) AF: 0.214 AC: 451 AN: 2104

Alfa AF: 0.221 Hom.: 4289

Bravo AF: 0.263

Asia WGS AF: 0.202 AC: 702 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.60
PhyloP100		-0.97

Splicing

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

Other links and lift over

dbSNP: rs752590; hg19: chr2-113972945;