18-3488153-G-A

Position:

• chr18-3488153-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 0.418 in 151,906 control chromosomes in the GnomAD database, including 13,771 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 0.42 (13771 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.466 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63425 AN: 151788 Hom.: 13760 Cov.: 32

Gnomad AFR AF: 0.406

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.339

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.470

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.418 AC: 63472 AN: 151906 Hom.: 13771 Cov.: 32 AF XY: 0.409 AC XY: 30379 AN XY: 74236

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.418

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.470

Gnomad4 OTH AF: 0.394

Alfa AF: 0.439 Hom.: 30514

Bravo AF: 0.407

Asia WGS AF: 0.189 AC: 657 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	1.8
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs238129; hg19: chr18-3488151;