rs11598564

Variant names:

• chr10-101204847-G-A
• rs11598564

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 0.452 in 152,034 control chromosomes in the GnomAD database, including 15,602 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 0.45 (15602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.287
• Publications: 15 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 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: 0.452 AC: 68689 AN: 151916 Hom.: 15586 Cov.: 32

Gnomad AFR AF: 0.436

Gnomad AMI AF: 0.682

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.481

Gnomad OTH AF: 0.437

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

GnomAD4 genome AF: 0.452 AC: 68750 AN: 152034 Hom.: 15602 Cov.: 32 AF XY: 0.448 AC XY: 33315 AN XY: 74294

African (AFR) AF: 0.436 AC: 18084 AN: 41436

American (AMR) AF: 0.361 AC: 5514 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1725 AN: 3472

East Asian (EAS) AF: 0.482 AC: 2493 AN: 5170

South Asian (SAS) AF: 0.458 AC: 2213 AN: 4832

European-Finnish (FIN) AF: 0.412 AC: 4348 AN: 10542

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.481 AC: 32720 AN: 67980

Other (OTH) AF: 0.435 AC: 919 AN: 2114

Alfa AF: 0.469 Hom.: 72579

Bravo AF: 0.448

Asia WGS AF: 0.440 AC: 1526 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.11
DANN	Benign	0.55
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs11598564; hg19: chr10-102964604;