chr18-78703038-G-A

Variant names:

• chr18-78703038-G-A
• rs11659609

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;