rs11052552

Positions:

• chr12-9703362-T-G

Variant summary

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

The variant allele was found at a frequency of 0.428 in 150,832 control chromosomes in the GnomAD database, including 15,235 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 0.43 (15235 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.598 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.9703362T>G		intergenic_region
LINC02390	XR_931347.3	n.-22T>G		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLECL1P	ENST00000702603.1	n.320-922A>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.428 AC: 64579 AN: 150726 Hom.: 15231 Cov.: 31

Gnomad AFR AF: 0.213

Gnomad AMI AF: 0.543

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.617

Gnomad SAS AF: 0.498

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.518

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.428 AC: 64594 AN: 150832 Hom.: 15235 Cov.: 31 AF XY: 0.426 AC XY: 31413 AN XY: 73682

Gnomad4 AFR AF: 0.213

Gnomad4 AMR AF: 0.507

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.616

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.518

Gnomad4 OTH AF: 0.457

Alfa AF: 0.503 Hom.: 13282

Bravo AF: 0.426

Asia WGS AF: 0.538 AC: 1868 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11052552; hg19: chr12-9855958;