8-57029799-C-T

Position:

• chr8-57029799-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 0.453 in 151,798 control chromosomes in the GnomAD database, including 16,187 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 0.45 (16187 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.08

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.563 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: 0.453 AC: 68721 AN: 151680 Hom.: 16140 Cov.: 31

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.517

Gnomad SAS AF: 0.494

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.465

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

GnomAD4 genome AF: 0.453 AC: 68821 AN: 151798 Hom.: 16187 Cov.: 31 AF XY: 0.455 AC XY: 33776 AN XY: 74176

Gnomad4 AFR AF: 0.569

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.419

Gnomad4 EAS AF: 0.517

Gnomad4 SAS AF: 0.492

Gnomad4 FIN AF: 0.343

Gnomad4 NFE AF: 0.388

Gnomad4 OTH AF: 0.466

Alfa AF: 0.405 Hom.: 21104

Bravo AF: 0.470

Asia WGS AF: 0.493 AC: 1713 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2119783; hg19: chr8-57942358;