11-31846153-G-A

Variant names:

• chr11-31846153-G-A
• rs685428
• ENST00000532942.5:c.101+29514G>A

Variant summary

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

The ENST00000532942.5(ENSG00000285283):​c.101+29514G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.822 in 152,122 control chromosomes in the GnomAD database, including 51,929 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 0.82 (51929 hom., cov: 32)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.317
• Publications: 4 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=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.91 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PAX6-AS1	NR_033971.1		n.74+29514G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285283	ENST00000532942.5	TSL:2	c.101+29514G>A		intron	N/A	ENSP00000436422.1
	PAUPAR	ENST00000506388.2	TSL:1	n.74+29514G>A		intron	N/A
	ENSG00000285283	ENST00000530348.5	TSL:4	c.-245+33656G>A		intron	N/A	ENSP00000436482.1

Frequencies

GnomAD3 genomes AF: 0.822 AC: 124962 AN: 152004 Hom.: 51870 Cov.: 32

Gnomad AFR AF: 0.918

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.747

Gnomad ASJ AF: 0.770

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.772

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

GnomAD4 genome AF: 0.822 AC: 125073 AN: 152122 Hom.: 51929 Cov.: 32 AF XY: 0.821 AC XY: 61036 AN XY: 74358

African (AFR) AF: 0.918 AC: 38133 AN: 41532

American (AMR) AF: 0.747 AC: 11410 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.770 AC: 2672 AN: 3470

East Asian (EAS) AF: 0.587 AC: 3023 AN: 5150

South Asian (SAS) AF: 0.709 AC: 3417 AN: 4822

European-Finnish (FIN) AF: 0.863 AC: 9125 AN: 10574

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54719 AN: 67986

Other (OTH) AF: 0.764 AC: 1615 AN: 2114

Alfa AF: 0.819 Hom.: 8790

Bravo AF: 0.813

Asia WGS AF: 0.633 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.60
DANN	Benign	0.22
PhyloP100		-0.32
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: rs685428; hg19: chr11-31867699;