8-75840555-A-G

Variant names:

• chr8-75840555-A-G
• rs1531462

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 0.919 in 152,214 control chromosomes in the GnomAD database, including 64,452 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 0.92 (64452 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.876
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.919 AC: 139730 AN: 152096 Hom.: 64388 Cov.: 32

Gnomad AFR AF: 0.981

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.932

Gnomad ASJ AF: 0.913

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.946

Gnomad FIN AF: 0.827

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.920

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

GnomAD4 genome AF: 0.919 AC: 139854 AN: 152214 Hom.: 64452 Cov.: 32 AF XY: 0.916 AC XY: 68127 AN XY: 74392

African (AFR) AF: 0.981 AC: 40772 AN: 41572

American (AMR) AF: 0.932 AC: 14252 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.913 AC: 3171 AN: 3472

East Asian (EAS) AF: 0.998 AC: 5145 AN: 5156

South Asian (SAS) AF: 0.946 AC: 4566 AN: 4826

European-Finnish (FIN) AF: 0.827 AC: 8745 AN: 10578

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 60218 AN: 68002

Other (OTH) AF: 0.921 AC: 1943 AN: 2110

Alfa AF: 0.896 Hom.: 42056

Bravo AF: 0.931

Asia WGS AF: 0.970 AC: 3373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.13
DANN	Benign	0.54
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs1531462; hg19: chr8-76752790;