rs12286701

Positions:

• chr11-31841814-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000532942.5(ENSG00000285283):​c.101+25175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0777 in 152,282 control chromosomes in the GnomAD database, including 802 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 0.078 (802 hom., cov: 32)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.177

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX6-AS1	NR_033971.1	n.74+25175T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5	c.101+25175T>C		intron_variant		2		ENSP00000436422.1

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11825 AN: 152164 Hom.: 800 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0468

Gnomad ASJ AF: 0.0786

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0719

Gnomad FIN AF: 0.0393

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0400

Gnomad OTH AF: 0.0736

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

GnomAD4 genome AF: 0.0777 AC: 11838 AN: 152282 Hom.: 802 Cov.: 32 AF XY: 0.0777 AC XY: 5784 AN XY: 74468

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0786

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0709

Gnomad4 FIN AF: 0.0393

Gnomad4 NFE AF: 0.0400

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0590 Hom.: 124

Bravo AF: 0.0807

Asia WGS AF: 0.0610 AC: 210 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12286701; hg19: chr11-31863361;