8-20501107-C-T

Position:

• chr8-20501107-C-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 0.207 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.193

Genes affected

(HGNC:):

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/exons	MANE	Protein	UniProt
		n.20501107C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;