8-117770647-C-T

Variant names:

• chr8-117770647-C-T
• rs4876386

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 0.746 in 151,812 control chromosomes in the GnomAD database, including 42,529 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 0.75 (42529 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.808 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: 0.746 AC: 113149 AN: 151694 Hom.: 42482 Cov.: 30

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.694

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.788

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.804

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.715

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.746 AC: 113251 AN: 151812 Hom.: 42529 Cov.: 30 AF XY: 0.750 AC XY: 55626 AN XY: 74198

Gnomad4 AFR AF: 0.815

Gnomad4 AMR AF: 0.672

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.789

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.804

Gnomad4 NFE AF: 0.714

Gnomad4 OTH AF: 0.677

Alfa AF: 0.742 Hom.: 5241

Bravo AF: 0.737

Asia WGS AF: 0.765 AC: 2639 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.24

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4876386; hg19: chr8-118782886;