rs12363572

Variant names:

• chr11-68621498-C-T
• rs12363572

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.0898 AC: 3727 AN: 41496

American (AMR) AF: 0.0910 AC: 1392 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3470

East Asian (EAS) AF: 0.0752 AC: 389 AN: 5176

South Asian (SAS) AF: 0.0681 AC: 329 AN: 4830

European-Finnish (FIN) AF: 0.0877 AC: 927 AN: 10566

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7549 AN: 67986

Other (OTH) AF: 0.123 AC: 260 AN: 2112

Alfa AF: 0.103 Hom.: 143

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs12363572; hg19: chr11-68388966; COSMIC: COSV107549972;