rs11031492

Variant names:

• chr11-31863373-T-G
• rs11031492
• ENST00000532942.5:c.101+46734T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532942.5(ENSG00000285283):​c.101+46734T>G variant causes a intron 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: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0440
• Publications: 1 publications found

Genes affected

ENSG00000285283 (HGNC:):

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:53448): (PAX6 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PAX6-AS1	NR_033971.1	n.75-21921T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5	c.101+46734T>G		intron_variant	Intron 1 of 5	2		ENSP00000436422.1

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

African (AFR) AF: 0.0455 AC: 1891 AN: 41540

American (AMR) AF: 0.154 AC: 2359 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.0540 AC: 280 AN: 5188

South Asian (SAS) AF: 0.241 AC: 1159 AN: 4810

European-Finnish (FIN) AF: 0.279 AC: 2957 AN: 10584

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.182 AC: 12345 AN: 67998

Other (OTH) AF: 0.129 AC: 271 AN: 2102

Alfa AF: 0.137 Hom.: 1056

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
PhyloP100		-0.044
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11031492; hg19: chr11-31884919;