rs3017365

Positions:

• chr18-62396108-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;