chr10-8079488-A-G

Position:

• chr10-8079488-A-G

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 0.841 in 149,352 control chromosomes in the GnomAD database, including 52,909 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 0.84 (52909 hom., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.926 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: 0.841 AC: 125454 AN: 149240 Hom.: 52868 Cov.: 23

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.863

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.924

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.840

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

GnomAD4 genome AF: 0.841 AC: 125548 AN: 149352 Hom.: 52909 Cov.: 23 AF XY: 0.846 AC XY: 61452 AN XY: 72646

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.863

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.919

Gnomad4 FIN AF: 0.924

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.842

Alfa AF: 0.848 Hom.: 51192

Bravo AF: 0.836

Asia WGS AF: 0.907 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs434645; hg19: chr10-8121451;