8-57029799-C-T

Variant names:

• chr8-57029799-C-T
• rs2119783

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;