rs685428

Positions:

• chr11-31846153-G-A
• chr11-31846153-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX6-AS1	NR_033971.1	n.74+29514G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5	c.101+29514G>A		intron_variant		2		ENSP00000436422.1

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

Gnomad4 AFR AF: 0.918

Gnomad4 AMR AF: 0.747

Gnomad4 ASJ AF: 0.770

Gnomad4 EAS AF: 0.587

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.863

Gnomad4 NFE AF: 0.805

Gnomad4 OTH AF: 0.764

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.60
DANN	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs685428; hg19: chr11-31867699;