10-8079488-A-G

Variant names:

• chr10-8079488-A-G
• rs434645

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.782 AC: 31542 AN: 40334

American (AMR) AF: 0.863 AC: 12907 AN: 14956

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3192 AN: 3464

East Asian (EAS) AF: 0.948 AC: 4771 AN: 5032

South Asian (SAS) AF: 0.919 AC: 4295 AN: 4674

European-Finnish (FIN) AF: 0.924 AC: 9178 AN: 9936

Middle Eastern (MID) AF: 0.888 AC: 261 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 56812 AN: 67688

Other (OTH) AF: 0.842 AC: 1741 AN: 2068

Alfa AF: 0.846 Hom.: 76766

Bravo AF: 0.836

Asia WGS AF: 0.907 AC: 3152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.32
DANN	Benign	0.37
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs434645; hg19: chr10-8121451;