18-65364000-G-T

Variant names:

• chr18-65364000-G-T
• rs470490

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 0.697 in 152,048 control chromosomes in the GnomAD database, including 37,848 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 0.70 (37848 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.18

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.85 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: 0.697 AC: 105948 AN: 151928 Hom.: 37799 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.695

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.658

Gnomad EAS AF: 0.559

Gnomad SAS AF: 0.709

Gnomad FIN AF: 0.653

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.690

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

GnomAD4 genome AF: 0.697 AC: 106048 AN: 152048 Hom.: 37848 Cov.: 31 AF XY: 0.702 AC XY: 52166 AN XY: 74322

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.658

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.653

Gnomad4 NFE AF: 0.611

Gnomad4 OTH AF: 0.693

Alfa AF: 0.628 Hom.: 48956

Bravo AF: 0.707

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs470490; hg19: chr18-63031236;