rs11564299

Variant names:

• chr18-28180064-A-G
• rs11564299

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 0.17 in 152,190 control chromosomes in the GnomAD database, including 2,677 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 0.17 (2677 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.228 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: 0.170 AC: 25797 AN: 152072 Hom.: 2678 Cov.: 33

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.0824

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.0296

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.211

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.231

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.170 AC: 25801 AN: 152190 Hom.: 2677 Cov.: 33 AF XY: 0.168 AC XY: 12488 AN XY: 74432

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.215

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.0297

Gnomad4 SAS AF: 0.145

Gnomad4 FIN AF: 0.211

Gnomad4 NFE AF: 0.231

Gnomad4 OTH AF: 0.154

Alfa AF: 0.185 Hom.: 257

Bravo AF: 0.164

Asia WGS AF: 0.0900 AC: 313 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	15
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11564299; hg19: chr18-25760028;