rs3114267

chr18-59779189-C-Gchr18-59779189-C-T

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 0.269 in 152,082 control chromosomes in the GnomAD database, including 5,969 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 0.27 (5969 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 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: 0.269 AC: 40826 AN: 151964 Hom.: 5956 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.210

Gnomad AMR AF: 0.256

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.0749

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.244

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.269 AC: 40880 AN: 152082 Hom.: 5969 Cov.: 33 AF XY: 0.262 AC XY: 19505 AN XY: 74340

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.186

Gnomad4 EAS AF: 0.0751

Gnomad4 SAS AF: 0.121

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.244

Gnomad4 OTH AF: 0.273

Alfa AF: 0.0842 Hom.: 109

Bravo AF: 0.279

Asia WGS AF: 0.131 AC: 456 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	7.3
Dann	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3114267; hg19: chr18-57446421;