18-68543152-A-G

Variant names:

• chr18-68543152-A-G
• rs574539

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.393 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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.401

Gnomad4 ASJ AF: 0.525

Gnomad4 EAS AF: 0.614

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.433

Gnomad4 NFE AF: 0.419

Gnomad4 OTH AF: 0.390

Alfa AF: 0.413 Hom.: 17153

Bravo AF: 0.379

Asia WGS AF: 0.574 AC: 1993 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs574539; hg19: chr18-66210389;