rs677874

Variant names:

• chr11-31869757-G-T
• rs677874
• ENST00000532942.5:c.101+53118G>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+53118G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.815 in 152,204 control chromosomes in the GnomAD database, including 51,139 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 (51139 hom., cov: 33)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.613
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.908 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.75-15537G>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285283	ENST00000532942.5	TSL:2	c.101+53118G>T		intron	N/A	ENSP00000436422.1
	PAUPAR	ENST00000506388.2	TSL:1	n.75-15537G>T		intron	N/A
	ENSG00000285283	ENST00000530348.5	TSL:4	c.-245+57260G>T		intron	N/A	ENSP00000436482.1

Frequencies

GnomAD3 genomes AF: 0.815 AC: 123998 AN: 152086 Hom.: 51090 Cov.: 33

Gnomad AFR AF: 0.915

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.740

Gnomad ASJ AF: 0.762

Gnomad EAS AF: 0.583

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.831

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.768

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

GnomAD4 genome AF: 0.815 AC: 124097 AN: 152204 Hom.: 51139 Cov.: 33 AF XY: 0.812 AC XY: 60439 AN XY: 74424

African (AFR) AF: 0.915 AC: 38025 AN: 41540

American (AMR) AF: 0.740 AC: 11317 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.762 AC: 2644 AN: 3472

East Asian (EAS) AF: 0.583 AC: 3016 AN: 5176

South Asian (SAS) AF: 0.659 AC: 3178 AN: 4822

European-Finnish (FIN) AF: 0.831 AC: 8799 AN: 10592

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54636 AN: 68002

Other (OTH) AF: 0.759 AC: 1604 AN: 2112

Alfa AF: 0.801 Hom.: 190025

Bravo AF: 0.810

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.4
DANN	Benign	0.18
PhyloP100		-0.61
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: rs677874; hg19: chr11-31891303;