8-20501107-C-T

Variant names:

• chr8-20501107-C-T
• rs9785133

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 0.207 in 151,846 control chromosomes in the GnomAD database, including 4,569 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 0.21 (4569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.207 AC: 31428 AN: 151728 Hom.: 4556 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.123

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0460

Gnomad MID AF: 0.237

Gnomad NFE AF: 0.115

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.207 AC: 31507 AN: 151846 Hom.: 4569 Cov.: 32 AF XY: 0.202 AC XY: 15010 AN XY: 74210

Gnomad4 AFR AF: 0.403

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.149

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.209

Gnomad4 FIN AF: 0.0460

Gnomad4 NFE AF: 0.115

Gnomad4 OTH AF: 0.192

Alfa AF: 0.129 Hom.: 804

Bravo AF: 0.233

Asia WGS AF: 0.212 AC: 736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.0
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9785133; hg19: chr8-20358618;