rs525485

Variant names:

• chr11-118685045-G-A
• rs525485

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.315 in 151,772 control chromosomes in the GnomAD database, including 7,966 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 0.32 (7966 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 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: 0.315 AC: 47818 AN: 151654 Hom.: 7953 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.315 AC: 47850 AN: 151772 Hom.: 7966 Cov.: 32 AF XY: 0.316 AC XY: 23405 AN XY: 74170

African (AFR) AF: 0.239 AC: 9877 AN: 41380

American (AMR) AF: 0.458 AC: 6980 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2091 AN: 5150

South Asian (SAS) AF: 0.189 AC: 907 AN: 4798

European-Finnish (FIN) AF: 0.313 AC: 3284 AN: 10486

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22213 AN: 67938

Other (OTH) AF: 0.330 AC: 695 AN: 2108

Alfa AF: 0.324 Hom.: 1166

Bravo AF: 0.330

Asia WGS AF: 0.270 AC: 941 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	11
DANN	Benign	0.91
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs525485; hg19: chr11-118555754;