rs11175040

Variant names:

• chr12-63553914-C-T
• rs11175040

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 0.167 in 151,988 control chromosomes in the GnomAD database, including 2,352 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 0.17 (2352 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25299 AN: 151870 Hom.: 2338 Cov.: 32

Gnomad AFR AF: 0.219

Gnomad AMI AF: 0.197

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.156

Gnomad EAS AF: 0.00946

Gnomad SAS AF: 0.0896

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.162

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

GnomAD4 genome AF: 0.167 AC: 25344 AN: 151988 Hom.: 2352 Cov.: 32 AF XY: 0.166 AC XY: 12327 AN XY: 74302

African (AFR) AF: 0.220 AC: 9109 AN: 41436

American (AMR) AF: 0.124 AC: 1888 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.156 AC: 541 AN: 3464

East Asian (EAS) AF: 0.00948 AC: 49 AN: 5168

South Asian (SAS) AF: 0.0897 AC: 432 AN: 4818

European-Finnish (FIN) AF: 0.195 AC: 2059 AN: 10554

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10677 AN: 67948

Other (OTH) AF: 0.161 AC: 340 AN: 2110

Alfa AF: 0.158 Hom.: 1134

Bravo AF: 0.165

Asia WGS AF: 0.0610 AC: 211 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.62
DANN	Benign	0.61
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs11175040; hg19: chr12-63947694;