rs11031492

chr11-31863373-T-G

Variant summary

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

The NR_033971.1(PAX6-AS1):n.75-21921T>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 0.144 in 152,176 control chromosomes in the GnomAD database, including 1,990 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 0.14 (1990 hom., cov: 32)
• Consequence: PAX6-AS1 NR_033971.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.229 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PAX6-AS1	NR_033971.1	n.75-21921T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PAUPAR	ENST00000644607.1	n.375-21921T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21870 AN: 152058 Hom.: 1989 Cov.: 32

Gnomad AFR AF: 0.0455

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0537

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.279

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.182

Gnomad OTH AF: 0.131

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

GnomAD4 genome AF: 0.144 AC: 21880 AN: 152176 Hom.: 1990 Cov.: 32 AF XY: 0.148 AC XY: 11036 AN XY: 74396

Gnomad4 AFR AF: 0.0455

Gnomad4 AMR AF: 0.154

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0540

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.279

Gnomad4 NFE AF: 0.182

Gnomad4 OTH AF: 0.129

Alfa AF: 0.163 Hom.: 472

Bravo AF: 0.127

Asia WGS AF: 0.135 AC: 468 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.7
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11031492; hg19: chr11-31884919;