rs11067362

Variant names:

• chr12-115000277-T-C
• rs11067362

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 0.146 in 151,936 control chromosomes in the GnomAD database, including 2,445 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 0.15 (2445 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.309 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: 0.146 AC: 22178 AN: 151818 Hom.: 2437 Cov.: 31

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.0571

Gnomad EAS AF: 0.000776

Gnomad SAS AF: 0.0361

Gnomad FIN AF: 0.0847

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0861

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.146 AC: 22230 AN: 151936 Hom.: 2445 Cov.: 31 AF XY: 0.142 AC XY: 10568 AN XY: 74272

African (AFR) AF: 0.314 AC: 12972 AN: 41368

American (AMR) AF: 0.113 AC: 1718 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0571 AC: 198 AN: 3470

East Asian (EAS) AF: 0.000778 AC: 4 AN: 5142

South Asian (SAS) AF: 0.0356 AC: 171 AN: 4810

European-Finnish (FIN) AF: 0.0847 AC: 895 AN: 10572

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.0861 AC: 5852 AN: 67998

Other (OTH) AF: 0.129 AC: 272 AN: 2110

Alfa AF: 0.0956 Hom.: 520

Bravo AF: 0.156

Asia WGS AF: 0.0480 AC: 168 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	11
DANN	Benign	0.76
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs11067362; hg19: chr12-115438082;