rs11617488

Variant names:

• chr13-21619823-A-G
• rs11617488

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	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

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.361

Gnomad4 ASJ AF: 0.183

Gnomad4 EAS AF: 0.609

Gnomad4 SAS AF: 0.413

Gnomad4 FIN AF: 0.261

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.269

Alfa AF: 0.235 Hom.: 2088

Bravo AF: 0.284

Asia WGS AF: 0.498 AC: 1729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11617488; hg19: chr13-22193962;