13-21619823-A-G

Variant names:

• chr13-21619823-A-G
• rs11617488

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 0.276 in 152,026 control chromosomes in the GnomAD database, including 6,458 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 0.28 (6458 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.505
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.591 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: 0.275 AC: 41845 AN: 151908 Hom.: 6444 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.183

Gnomad EAS AF: 0.608

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.285

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.276 AC: 41896 AN: 152026 Hom.: 6458 Cov.: 32 AF XY: 0.286 AC XY: 21226 AN XY: 74330

African (AFR) AF: 0.315 AC: 13058 AN: 41438

American (AMR) AF: 0.361 AC: 5504 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 636 AN: 3470

East Asian (EAS) AF: 0.609 AC: 3149 AN: 5174

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4826

European-Finnish (FIN) AF: 0.261 AC: 2752 AN: 10560

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.205 AC: 13958 AN: 67988

Other (OTH) AF: 0.269 AC: 567 AN: 2108

Alfa AF: 0.234 Hom.: 2804

Bravo AF: 0.284

Asia WGS AF: 0.498 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	14
DANN	Benign	0.86
PhyloP100		0.51

Splicing

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

Other links and lift over

dbSNP: rs11617488; hg19: chr13-22193962;