18-65364000-G-T

Variant names:

• chr18-65364000-G-T
• rs470490

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 0.697 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
• Publications: 13 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.857 AC: 35574 AN: 41498

American (AMR) AF: 0.731 AC: 11158 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.658 AC: 2279 AN: 3464

East Asian (EAS) AF: 0.560 AC: 2879 AN: 5142

South Asian (SAS) AF: 0.709 AC: 3416 AN: 4818

European-Finnish (FIN) AF: 0.653 AC: 6914 AN: 10586

Middle Eastern (MID) AF: 0.718 AC: 211 AN: 294

European-Non Finnish (NFE) AF: 0.611 AC: 41521 AN: 67954

Other (OTH) AF: 0.693 AC: 1462 AN: 2110

Alfa AF: 0.638 Hom.: 114906

Bravo AF: 0.707

Asia WGS AF: 0.672 AC: 2337 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.52
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs470490; hg19: chr18-63031236;