18-42708328-C-T

Variant names:

• chr18-42708328-C-T
• rs8085804

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 0.463 in 151,942 control chromosomes in the GnomAD database, including 19,909 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 0.46 (19909 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.763 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: 0.463 AC: 70291 AN: 151822 Hom.: 19861 Cov.: 32

Gnomad AFR AF: 0.770

Gnomad AMI AF: 0.377

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.747

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.440

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

GnomAD4 genome AF: 0.463 AC: 70404 AN: 151942 Hom.: 19909 Cov.: 32 AF XY: 0.466 AC XY: 34559 AN XY: 74240

Gnomad4 AFR AF: 0.770

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.746

Gnomad4 SAS AF: 0.410

Gnomad4 FIN AF: 0.285

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.447

Alfa AF: 0.327 Hom.: 14322

Bravo AF: 0.496

Asia WGS AF: 0.607 AC: 2108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8085804; hg19: chr18-40288293;