rs11031497

Positions:

• chr11-31870709-G-A
• chr11-31870709-G-T

Variant summary

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

The NR_033971.1(PAX6-AS1):​n.75-14585G>A 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 0.352 in 151,972 control chromosomes in the GnomAD database, including 10,276 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 0.35 (10276 hom., cov: 31)
• Consequence: PAX6-AS1 NR_033971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940

Genes affected

PAUPAR (HGNC:49670): (PAX6 upstream antisense RNA) This gene is thought to produce a functional long non-coding RNA. Knockdown of this transcript results in genome-wide changes in gene expression, particularly of cell cyle genes, indicating a role in regulating differentiation. This transcript may bind to the promoter region of target genes and may also interact with the transcription factor Pax6 (paired box 6). [provided by RefSeq, Feb 2015]

PAX6-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX6-AS1	NR_033971.1	n.75-14585G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PAUPAR	ENST00000644607.1	n.375-14585G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.352 AC: 53481 AN: 151854 Hom.: 10267 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.355

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.526

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.352 AC: 53502 AN: 151972 Hom.: 10276 Cov.: 31 AF XY: 0.357 AC XY: 26517 AN XY: 74268

Gnomad4 AFR AF: 0.223

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.526

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.330

Alfa AF: 0.387 Hom.: 11315

Bravo AF: 0.332

Asia WGS AF: 0.304 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031497; hg19: chr11-31892255;