chr18-60275566-C-T

Variant names:

• chr18-60275566-C-T
• rs9956279

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 0.226 in 151,950 control chromosomes in the GnomAD database, including 4,547 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 0.23 (4547 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.335 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: 0.226 AC: 34322 AN: 151832 Hom.: 4546 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.310

Gnomad AMR AF: 0.187

Gnomad ASJ AF: 0.230

Gnomad EAS AF: 0.0551

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.255

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.226 AC: 34320 AN: 151950 Hom.: 4547 Cov.: 31 AF XY: 0.222 AC XY: 16463 AN XY: 74276

Gnomad4 AFR AF: 0.107

Gnomad4 AMR AF: 0.187

Gnomad4 ASJ AF: 0.230

Gnomad4 EAS AF: 0.0554

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.255

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.224

Alfa AF: 0.143 Hom.: 291

Bravo AF: 0.212

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.49
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9956279; hg19: chr18-57942799;