rs3764506

Variant names:

• chr18-74292238-C-T
• rs3764506

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 0.0158 in 152,296 control chromosomes in the GnomAD database, including 113 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 0.016 (113 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.175 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: 0.0158 AC: 2407 AN: 152178 Hom.: 113 Cov.: 33

Gnomad AFR AF: 0.0162

Gnomad AMI AF: 0.0263

Gnomad AMR AF: 0.0171

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.184

Gnomad SAS AF: 0.00993

Gnomad FIN AF: 0.0134

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.00406

Gnomad OTH AF: 0.0148

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

GnomAD4 genome AF: 0.0158 AC: 2412 AN: 152296 Hom.: 113 Cov.: 33 AF XY: 0.0169 AC XY: 1262 AN XY: 74466

Gnomad4 AFR AF: 0.0163

Gnomad4 AMR AF: 0.0172

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.184

Gnomad4 SAS AF: 0.00973

Gnomad4 FIN AF: 0.0134

Gnomad4 NFE AF: 0.00406

Gnomad4 OTH AF: 0.0137

Alfa AF: 0.0102 Hom.: 3

Bravo AF: 0.0186

Asia WGS AF: 0.0670 AC: 233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.47
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: rs3764506; hg19: chr18-71959473;