rs3017365

Variant names:

• chr18-62396108-G-A
• rs3017365

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 0.455 in 151,938 control chromosomes in the GnomAD database, including 16,509 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 0.45 (16509 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.504 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: 0.455 AC: 69038 AN: 151820 Hom.: 16514 Cov.: 31

Gnomad AFR AF: 0.442

Gnomad AMI AF: 0.474

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.0519

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.508

Gnomad OTH AF: 0.488

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

GnomAD4 genome AF: 0.455 AC: 69058 AN: 151938 Hom.: 16509 Cov.: 31 AF XY: 0.443 AC XY: 32889 AN XY: 74250

Gnomad4 AFR AF: 0.442

Gnomad4 AMR AF: 0.465

Gnomad4 ASJ AF: 0.505

Gnomad4 EAS AF: 0.0516

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.385

Gnomad4 NFE AF: 0.508

Gnomad4 OTH AF: 0.487

Alfa AF: 0.474 Hom.: 8838

Bravo AF: 0.462

Asia WGS AF: 0.226 AC: 791 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.4
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3017365; hg19: chr18-60063341;