rs3813065

Variant names:

• chr18-41954860-C-T
• rs3813065

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 0.203 in 152,172 control chromosomes in the GnomAD database, including 3,930 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 0.20 (3930 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.793

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 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: 0.203 AC: 30834 AN: 152054 Hom.: 3923 Cov.: 32

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.0912

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.107

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.166

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.180

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

GnomAD4 genome AF: 0.203 AC: 30873 AN: 152172 Hom.: 3930 Cov.: 32 AF XY: 0.203 AC XY: 15074 AN XY: 74374

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.107

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.113

Gnomad4 FIN AF: 0.166

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.183

Alfa AF: 0.141 Hom.: 1802

Bravo AF: 0.212

Asia WGS AF: 0.229 AC: 798 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.2
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3813065; hg19: chr18-39534825; COSMIC: COSV56275521;