rs12363572

Positions:

• chr11-68621498-C-T

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 0.1 in 152,134 control chromosomes in the GnomAD database, including 808 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 0.10 (808 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.188

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15251 AN: 152016 Hom.: 808 Cov.: 33

Gnomad AFR AF: 0.0899

Gnomad AMI AF: 0.219

Gnomad AMR AF: 0.0911

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0752

Gnomad SAS AF: 0.0685

Gnomad FIN AF: 0.0877

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.100 AC: 15252 AN: 152134 Hom.: 808 Cov.: 33 AF XY: 0.0981 AC XY: 7296 AN XY: 74374

Gnomad4 AFR AF: 0.0898

Gnomad4 AMR AF: 0.0910

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0752

Gnomad4 SAS AF: 0.0681

Gnomad4 FIN AF: 0.0877

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.123

Alfa AF: 0.103 Hom.: 141

Bravo AF: 0.102

Asia WGS AF: 0.0850 AC: 296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	6.7
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12363572; hg19: chr11-68388966;