rs11564299

chr18-28180064-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;