rs11853552

Variant names:

• chr15-32705381-G-A
• rs11853552

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 0.399 in 152,000 control chromosomes in the GnomAD database, including 13,420 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 0.40 (13420 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.89
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.502 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: 0.399 AC: 60646 AN: 151884 Hom.: 13411 Cov.: 33

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.421

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.544

Gnomad EAS AF: 0.0384

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.507

Gnomad OTH AF: 0.435

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

GnomAD4 genome AF: 0.399 AC: 60697 AN: 152000 Hom.: 13420 Cov.: 33 AF XY: 0.393 AC XY: 29205 AN XY: 74272

African (AFR) AF: 0.257 AC: 10658 AN: 41458

American (AMR) AF: 0.429 AC: 6553 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.544 AC: 1883 AN: 3462

East Asian (EAS) AF: 0.0384 AC: 199 AN: 5176

South Asian (SAS) AF: 0.258 AC: 1242 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4277 AN: 10540

Middle Eastern (MID) AF: 0.483 AC: 141 AN: 292

European-Non Finnish (NFE) AF: 0.507 AC: 34443 AN: 67950

Other (OTH) AF: 0.434 AC: 917 AN: 2114

Alfa AF: 0.469 Hom.: 62477

Bravo AF: 0.399

Asia WGS AF: 0.157 AC: 551 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	17
DANN	Benign	0.72
PhyloP100		2.9

Splicing

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

Other links and lift over

dbSNP: rs11853552; hg19: chr15-32997582;