chr18-25027759-G-A

Position:

• chr18-25027759-G-A

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 0.625 in 152,038 control chromosomes in the GnomAD database, including 30,385 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 0.63 (30385 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.470

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95046 AN: 151920 Hom.: 30392 Cov.: 33

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.705

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.695

Gnomad EAS AF: 0.606

Gnomad SAS AF: 0.626

Gnomad FIN AF: 0.563

Gnomad MID AF: 0.736

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.658

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

GnomAD4 genome AF: 0.625 AC: 95072 AN: 152038 Hom.: 30385 Cov.: 33 AF XY: 0.620 AC XY: 46104 AN XY: 74312

Gnomad4 AFR AF: 0.498

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.695

Gnomad4 EAS AF: 0.606

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.563

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.658

Alfa AF: 0.689 Hom.: 74360

Bravo AF: 0.627

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	6.7
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4800613; hg19: chr18-22607723;