8-133626015-G-T

Position:

• chr8-133626015-G-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 0.252 in 152,172 control chromosomes in the GnomAD database, including 5,338 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 0.25 (5338 hom., cov: 33)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.954

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.133626015G>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.252 AC: 38281 AN: 152054 Hom.: 5340 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.0267

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.298

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

GnomAD4 genome AF: 0.252 AC: 38297 AN: 152172 Hom.: 5338 Cov.: 33 AF XY: 0.249 AC XY: 18506 AN XY: 74394

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.221

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.0266

Gnomad4 SAS AF: 0.261

Gnomad4 FIN AF: 0.148

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.294

Alfa AF: 0.245 Hom.: 6420

Bravo AF: 0.259

Asia WGS AF: 0.150 AC: 523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.31
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3958181; hg19: chr8-134638258;