rs11069178

Variant names:

• chr12-118930022-A-C
• rs11069178

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 0.232 in 152,116 control chromosomes in the GnomAD database, including 4,059 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 0.23 (4059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.522
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 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: 0.232 AC: 35269 AN: 151998 Hom.: 4064 Cov.: 32

Gnomad AFR AF: 0.260

Gnomad AMI AF: 0.245

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.291

Gnomad FIN AF: 0.203

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.220

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.232 AC: 35267 AN: 152116 Hom.: 4059 Cov.: 32 AF XY: 0.232 AC XY: 17263 AN XY: 74362

African (AFR) AF: 0.260 AC: 10786 AN: 41486

American (AMR) AF: 0.197 AC: 3013 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.216 AC: 748 AN: 3468

East Asian (EAS) AF: 0.294 AC: 1518 AN: 5162

South Asian (SAS) AF: 0.289 AC: 1390 AN: 4814

European-Finnish (FIN) AF: 0.203 AC: 2152 AN: 10600

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.220 AC: 14927 AN: 67978

Other (OTH) AF: 0.207 AC: 438 AN: 2112

Alfa AF: 0.224 Hom.: 17145

Bravo AF: 0.228

Asia WGS AF: 0.283 AC: 981 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.43
DANN	Benign	0.74
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs11069178; hg19: chr12-119367827; COSMIC: COSV107182536;