rs11152213

Variant names:

• chr18-60185715-A-C
• rs11152213

Your query was ambiguous. Multiple possible variants found:

• chr18-60185715-A-C
• chr18-60185715-A-T

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 0.234 in 152,182 control chromosomes in the GnomAD database, including 4,283 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 (4283 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59
• Publications: 48 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.337 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.234 AC: 35536 AN: 152064 Hom.: 4280 Cov.: 33

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.183

Gnomad SAS AF: 0.349

Gnomad FIN AF: 0.171

Gnomad MID AF: 0.293

Gnomad NFE AF: 0.238

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.234 AC: 35570 AN: 152182 Hom.: 4283 Cov.: 33 AF XY: 0.230 AC XY: 17124 AN XY: 74396

African (AFR) AF: 0.265 AC: 10988 AN: 41526

American (AMR) AF: 0.159 AC: 2427 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 703 AN: 3468

East Asian (EAS) AF: 0.183 AC: 948 AN: 5184

South Asian (SAS) AF: 0.351 AC: 1694 AN: 4824

European-Finnish (FIN) AF: 0.171 AC: 1815 AN: 10602

Middle Eastern (MID) AF: 0.291 AC: 85 AN: 292

European-Non Finnish (NFE) AF: 0.238 AC: 16152 AN: 67968

Other (OTH) AF: 0.226 AC: 478 AN: 2116

Alfa AF: 0.229 Hom.: 10375

Bravo AF: 0.232

Asia WGS AF: 0.224 AC: 779 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.32
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs11152213; hg19: chr18-57852948;