18-68543152-A-G

Variant names:

• chr18-68543152-A-G
• rs574539

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.393 in 151,922 control chromosomes in the GnomAD database, including 12,313 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 0.39 (12313 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0130
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.29).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.596 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: 0.393 AC: 59658 AN: 151804 Hom.: 12306 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.401

Gnomad ASJ AF: 0.525

Gnomad EAS AF: 0.614

Gnomad SAS AF: 0.588

Gnomad FIN AF: 0.433

Gnomad MID AF: 0.401

Gnomad NFE AF: 0.419

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.393 AC: 59671 AN: 151922 Hom.: 12313 Cov.: 32 AF XY: 0.400 AC XY: 29683 AN XY: 74224

African (AFR) AF: 0.276 AC: 11435 AN: 41424

American (AMR) AF: 0.401 AC: 6121 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.525 AC: 1822 AN: 3468

East Asian (EAS) AF: 0.614 AC: 3159 AN: 5144

South Asian (SAS) AF: 0.589 AC: 2830 AN: 4806

European-Finnish (FIN) AF: 0.433 AC: 4575 AN: 10556

Middle Eastern (MID) AF: 0.387 AC: 113 AN: 292

European-Non Finnish (NFE) AF: 0.419 AC: 28494 AN: 67944

Other (OTH) AF: 0.390 AC: 825 AN: 2114

Alfa AF: 0.410 Hom.: 37540

Bravo AF: 0.379

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		-0.013

Splicing

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

Other links and lift over

dbSNP: rs574539; hg19: chr18-66210389;