chr8-119532708-C-T

Position:

• chr8-119532708-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 0.385 in 151,820 control chromosomes in the GnomAD database, including 12,397 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 0.38 (12397 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.557 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: 0.385 AC: 58368 AN: 151702 Hom.: 12397 Cov.: 31

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.534

Gnomad AMR AF: 0.469

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.338

Gnomad SAS AF: 0.575

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.385 AC: 58390 AN: 151820 Hom.: 12397 Cov.: 31 AF XY: 0.393 AC XY: 29147 AN XY: 74174

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.469

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.338

Gnomad4 SAS AF: 0.575

Gnomad4 FIN AF: 0.519

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.394

Alfa AF: 0.423 Hom.: 19013

Bravo AF: 0.366

Asia WGS AF: 0.482 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.7
DANN	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6993464; hg19: chr8-120544948;