rs11659463

Variant names:

• chr18-47952668-G-A
• rs11659463

Your query was ambiguous. Multiple possible variants found:

• chr18-47952668-G-A
• chr18-47952668-G-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 0.373 in 151,946 control chromosomes in the GnomAD database, including 11,082 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 0.37 (11082 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.173
• 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 (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56625 AN: 151826 Hom.: 11081 Cov.: 32

Gnomad AFR AF: 0.258

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.435

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.373 AC: 56636 AN: 151946 Hom.: 11082 Cov.: 32 AF XY: 0.371 AC XY: 27544 AN XY: 74262

African (AFR) AF: 0.258 AC: 10669 AN: 41396

American (AMR) AF: 0.342 AC: 5220 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1223 AN: 3466

East Asian (EAS) AF: 0.477 AC: 2467 AN: 5172

South Asian (SAS) AF: 0.494 AC: 2377 AN: 4810

European-Finnish (FIN) AF: 0.373 AC: 3934 AN: 10552

Middle Eastern (MID) AF: 0.342 AC: 100 AN: 292

European-Non Finnish (NFE) AF: 0.435 AC: 29535 AN: 67954

Other (OTH) AF: 0.375 AC: 793 AN: 2112

Alfa AF: 0.417 Hom.: 2779

Bravo AF: 0.361

Asia WGS AF: 0.454 AC: 1579 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.71
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs11659463; hg19: chr18-45479039;