11-31856454-T-C

Position:

• chr11-31856454-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+39815T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,108 control chromosomes in the GnomAD database, including 52,295 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 (52295 hom., cov: 31)
• Consequence: ENSG00000285283 ENST00000532942.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0110

Genes affected

ENSG00000285283 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PAX6-AS1	NR_033971.1	n.75-28840T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000285283	ENST00000532942.5	c.101+39815T>C		intron_variant		2		ENSP00000436422.1

Frequencies

GnomAD3 genomes AF: 0.824 AC: 125288 AN: 151992 Hom.: 52244 Cov.: 31

Gnomad AFR AF: 0.932

Gnomad AMI AF: 0.810

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.710

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.788

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.824 AC: 125390 AN: 152108 Hom.: 52295 Cov.: 31 AF XY: 0.823 AC XY: 61201 AN XY: 74388

Gnomad4 AFR AF: 0.932

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.768

Gnomad4 EAS AF: 0.580

Gnomad4 SAS AF: 0.711

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.803

Gnomad4 OTH AF: 0.761

Alfa AF: 0.794 Hom.: 60906

Bravo AF: 0.815

Asia WGS AF: 0.634 AC: 2207 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.1
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs761453; hg19: chr11-31878000;