rs11031497

Variant names:

• chr11-31870709-G-A
• rs11031497
• ENST00000532942.5:c.101+54070G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000532942.5(ENSG00000285283):​c.101+54070G>A variant causes a intron 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: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0940
• Publications: 7 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.412 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532942.5. 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
	PAX6-AS1	NR_033971.1		n.75-14585G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285283	ENST00000532942.5	TSL:2	c.101+54070G>A		intron	N/A	ENSP00000436422.1
	PAUPAR	ENST00000506388.2	TSL:1	n.75-14585G>A		intron	N/A
	ENSG00000285283	ENST00000530348.5	TSL:4	c.-245+58212G>A		intron	N/A	ENSP00000436482.1	E9PP27

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

African (AFR) AF: 0.223 AC: 9253 AN: 41438

American (AMR) AF: 0.355 AC: 5426 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1143 AN: 5160

South Asian (SAS) AF: 0.389 AC: 1872 AN: 4814

European-Finnish (FIN) AF: 0.526 AC: 5537 AN: 10536

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28292 AN: 67964

Other (OTH) AF: 0.330 AC: 695 AN: 2106

Alfa AF: 0.380 Hom.: 14410

Bravo AF: 0.332

Asia WGS AF: 0.304 AC: 1061 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.9
DANN	Benign	0.95
PhyloP100		-0.094
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11031497;

hg19: chr11-31892255;