rs11659609

Positions:

• chr18-78703038-G-A

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 0.281 in 152,040 control chromosomes in the GnomAD database, including 6,480 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 (6480 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.291

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42749 AN: 151922 Hom.: 6477 Cov.: 33

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.339

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.231

Gnomad EAS AF: 0.624

Gnomad SAS AF: 0.375

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.262

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

GnomAD4 genome AF: 0.281 AC: 42781 AN: 152040 Hom.: 6480 Cov.: 33 AF XY: 0.285 AC XY: 21163 AN XY: 74318

Gnomad4 AFR AF: 0.264

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.231

Gnomad4 EAS AF: 0.624

Gnomad4 SAS AF: 0.375

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.260

Gnomad4 OTH AF: 0.263

Alfa AF: 0.270 Hom.: 3187

Bravo AF: 0.282

Asia WGS AF: 0.488 AC: 1693 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	6.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11659609; hg19: chr18-76463038;