18-62414860-A-G

Variant names:

• chr18-62414860-A-G
• rs3018362

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.66 in 151,972 control chromosomes in the GnomAD database, including 34,077 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 0.66 (34077 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00
• Publications: 61 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.773 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: 0.660 AC: 100272 AN: 151854 Hom.: 34034 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.493

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.711

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.637

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.660 AC: 100363 AN: 151972 Hom.: 34077 Cov.: 31 AF XY: 0.653 AC XY: 48501 AN XY: 74270

African (AFR) AF: 0.780 AC: 32348 AN: 41464

American (AMR) AF: 0.626 AC: 9548 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.711 AC: 2466 AN: 3468

East Asian (EAS) AF: 0.284 AC: 1463 AN: 5154

South Asian (SAS) AF: 0.677 AC: 3260 AN: 4818

European-Finnish (FIN) AF: 0.558 AC: 5877 AN: 10532

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.637 AC: 43320 AN: 67964

Other (OTH) AF: 0.672 AC: 1416 AN: 2106

Alfa AF: 0.641 Hom.: 131193

Bravo AF: 0.669

Asia WGS AF: 0.496 AC: 1727 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.34
DANN	Benign	0.55
PhyloP100		-3.0

Splicing

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

Other links and lift over

dbSNP: rs3018362; hg19: chr18-60082093;