rs1806180

Variant names:

• chr11-31818717-G-A
• rs1806180
• ENST00000532942.5:c.101+2078G>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+2078G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 152,240 control chromosomes in the GnomAD database, including 3,065 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 0.20 (3065 hom., cov: 34)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.01
• Publications: 11 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.284 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.74+2078G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285283	ENST00000532942.5	TSL:2	c.101+2078G>A		intron	N/A	ENSP00000436422.1
	PAUPAR	ENST00000506388.2	TSL:1	n.74+2078G>A		intron	N/A
	ENSG00000285283	ENST00000530348.5	TSL:4	c.-245+6220G>A		intron	N/A	ENSP00000436482.1	E9PP27

Frequencies

GnomAD3 genomes AF: 0.196 AC: 29850 AN: 152122 Hom.: 3063 Cov.: 34

Gnomad AFR AF: 0.228

Gnomad AMI AF: 0.124

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.184

Gnomad FIN AF: 0.199

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.175

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.196 AC: 29883 AN: 152240 Hom.: 3065 Cov.: 34 AF XY: 0.196 AC XY: 14621 AN XY: 74444

African (AFR) AF: 0.228 AC: 9455 AN: 41538

American (AMR) AF: 0.202 AC: 3091 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 421 AN: 3470

East Asian (EAS) AF: 0.296 AC: 1533 AN: 5180

South Asian (SAS) AF: 0.184 AC: 889 AN: 4824

European-Finnish (FIN) AF: 0.199 AC: 2105 AN: 10600

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.175 AC: 11889 AN: 68008

Other (OTH) AF: 0.167 AC: 352 AN: 2110

Alfa AF: 0.179 Hom.: 1245

Bravo AF: 0.198

Asia WGS AF: 0.220 AC: 764 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.8
DANN	Benign	0.45
PhyloP100		1.0
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: rs1806180; hg19: chr11-31840265;