chr8-107142389-G-A

Variant names:

• chr8-107142389-G-A
• rs1892764

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 0.685 in 151,830 control chromosomes in the GnomAD database, including 35,619 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 0.69 (35619 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.605
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.73 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: 0.685 AC: 103899 AN: 151712 Hom.: 35574 Cov.: 32

Gnomad AFR AF: 0.682

Gnomad AMI AF: 0.460

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.665

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.657

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.698

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

GnomAD4 genome AF: 0.685 AC: 104004 AN: 151830 Hom.: 35619 Cov.: 32 AF XY: 0.681 AC XY: 50556 AN XY: 74204

African (AFR) AF: 0.682 AC: 28250 AN: 41422

American (AMR) AF: 0.741 AC: 11293 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2294 AN: 3464

East Asian (EAS) AF: 0.665 AC: 3414 AN: 5134

South Asian (SAS) AF: 0.616 AC: 2971 AN: 4826

European-Finnish (FIN) AF: 0.657 AC: 6933 AN: 10552

Middle Eastern (MID) AF: 0.724 AC: 213 AN: 294

European-Non Finnish (NFE) AF: 0.689 AC: 46746 AN: 67888

Other (OTH) AF: 0.698 AC: 1471 AN: 2108

Alfa AF: 0.702 Hom.: 6351

Bravo AF: 0.692

Asia WGS AF: 0.648 AC: 2255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	7.3
DANN	Benign	0.59
PhyloP100		0.60

Splicing

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

Other links and lift over

dbSNP: rs1892764; hg19: chr8-108154617;