8-29424533-A-G

Variant names:

• chr8-29424533-A-G
• rs654418

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 0.91 in 152,282 control chromosomes in the GnomAD database, including 63,244 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 0.91 (63244 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.792
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.937 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: 0.910 AC: 138545 AN: 152164 Hom.: 63202 Cov.: 32

Gnomad AFR AF: 0.866

Gnomad AMI AF: 0.883

Gnomad AMR AF: 0.949

Gnomad ASJ AF: 0.895

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.934

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.937

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.910 AC: 138645 AN: 152282 Hom.: 63244 Cov.: 32 AF XY: 0.909 AC XY: 67711 AN XY: 74452

African (AFR) AF: 0.866 AC: 35983 AN: 41552

American (AMR) AF: 0.949 AC: 14527 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.895 AC: 3107 AN: 3472

East Asian (EAS) AF: 0.816 AC: 4233 AN: 5190

South Asian (SAS) AF: 0.854 AC: 4116 AN: 4820

European-Finnish (FIN) AF: 0.934 AC: 9907 AN: 10608

Middle Eastern (MID) AF: 0.932 AC: 274 AN: 294

European-Non Finnish (NFE) AF: 0.937 AC: 63758 AN: 68022

Other (OTH) AF: 0.916 AC: 1935 AN: 2112

Alfa AF: 0.919 Hom.: 24305

Bravo AF: 0.911

Asia WGS AF: 0.839 AC: 2918 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.19
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs654418; hg19: chr8-29282050;