8-143087674-G-A

Variant names:

• chr8-143087674-G-A
• rs4246828

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 0.656 in 152,134 control chromosomes in the GnomAD database, including 35,088 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 0.66 (35088 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.777
• Publications: 16 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.841 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99792 AN: 152016 Hom.: 35068 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.885

Gnomad AMR AF: 0.779

Gnomad ASJ AF: 0.768

Gnomad EAS AF: 0.861

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.656 AC: 99855 AN: 152134 Hom.: 35088 Cov.: 33 AF XY: 0.664 AC XY: 49405 AN XY: 74386

African (AFR) AF: 0.379 AC: 15732 AN: 41468

American (AMR) AF: 0.779 AC: 11913 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.768 AC: 2666 AN: 3472

East Asian (EAS) AF: 0.862 AC: 4462 AN: 5178

South Asian (SAS) AF: 0.788 AC: 3801 AN: 4824

European-Finnish (FIN) AF: 0.778 AC: 8228 AN: 10582

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.744 AC: 50610 AN: 68002

Other (OTH) AF: 0.674 AC: 1424 AN: 2114

Alfa AF: 0.730 Hom.: 148508

Bravo AF: 0.647

Asia WGS AF: 0.776 AC: 2694 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.12
DANN	Benign	0.76
PhyloP100		0.78

Splicing

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

Other links and lift over

dbSNP: rs4246828; hg19: chr8-144169091;