rs8084125

Variant names:

• chr18-77240802-T-C
• rs8084125

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 0.136 in 152,246 control chromosomes in the GnomAD database, including 1,567 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 0.14 (1567 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.662

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.166 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: 0.136 AC: 20715 AN: 152128 Hom.: 1570 Cov.: 32

Gnomad AFR AF: 0.0925

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.118

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.177

Gnomad FIN AF: 0.193

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.164

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.136 AC: 20714 AN: 152246 Hom.: 1567 Cov.: 32 AF XY: 0.137 AC XY: 10191 AN XY: 74416

Gnomad4 AFR AF: 0.0926

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.193

Gnomad4 NFE AF: 0.164

Gnomad4 OTH AF: 0.135

Alfa AF: 0.160 Hom.: 2596

Bravo AF: 0.128

Asia WGS AF: 0.0750 AC: 262 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	7.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8084125; hg19: chr18-74952758;