8-133989625-T-C

Position:

• chr8-133989625-T-C

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 0.315 in 151,950 control chromosomes in the GnomAD database, including 8,225 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 0.32 (8225 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.122

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.431 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47833 AN: 151832 Hom.: 8220 Cov.: 31

Gnomad AFR AF: 0.437

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.310

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.315 AC: 47874 AN: 151950 Hom.: 8225 Cov.: 31 AF XY: 0.309 AC XY: 22922 AN XY: 74268

Gnomad4 AFR AF: 0.437

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.214

Gnomad4 FIN AF: 0.310

Gnomad4 NFE AF: 0.293

Gnomad4 OTH AF: 0.315

Alfa AF: 0.268 Hom.: 2600

Bravo AF: 0.311

Asia WGS AF: 0.115 AC: 402 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.4
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: rs1119729; hg19: chr8-135001868;