8-107854594-C-T

Position:

• chr8-107854594-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.266 in 151,958 control chromosomes in the GnomAD database, including 6,671 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 0.27 (6671 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.400

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.3).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.364 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: 0.266 AC: 40378 AN: 151840 Hom.: 6671 Cov.: 31

Gnomad AFR AF: 0.0982

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.0253

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.266 AC: 40388 AN: 151958 Hom.: 6671 Cov.: 31 AF XY: 0.264 AC XY: 19573 AN XY: 74244

Gnomad4 AFR AF: 0.0981

Gnomad4 AMR AF: 0.237

Gnomad4 ASJ AF: 0.352

Gnomad4 EAS AF: 0.0256

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.368

Gnomad4 OTH AF: 0.290

Alfa AF: 0.350 Hom.: 20275

Bravo AF: 0.250

Asia WGS AF: 0.166 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.30
CADD	Benign	15
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: rs17309585; hg19: chr8-108866822;