18-9287342-G-T

Position:

• chr18-9287342-G-T

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 0.426 in 151,824 control chromosomes in the GnomAD database, including 16,083 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 0.43 (16083 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.820

ACMG classification

Verdict is Benign. Variant got -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 = 0.68 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: 0.426 AC: 64588 AN: 151706 Hom.: 16043 Cov.: 31

Gnomad AFR AF: 0.686

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.393

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.426 AC: 64672 AN: 151824 Hom.: 16083 Cov.: 31 AF XY: 0.424 AC XY: 31489 AN XY: 74236

Gnomad4 AFR AF: 0.687

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.393

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.565

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.420

Alfa AF: 0.332 Hom.: 9014

Bravo AF: 0.446

Asia WGS AF: 0.492 AC: 1710 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	0.68
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2083845; hg19: chr18-9287340;