rs3813065

Positions:

• chr18-41954860-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 0.203 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;