chr8-78108465-G-A

Variant names:

• chr8-78108465-G-A
• rs7357405

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 0.505 in 152,000 control chromosomes in the GnomAD database, including 20,095 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 0.50 (20095 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.64 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: 0.505 AC: 76625 AN: 151882 Hom.: 20059 Cov.: 33

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.374

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.487

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.453

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.505 AC: 76712 AN: 152000 Hom.: 20095 Cov.: 33 AF XY: 0.497 AC XY: 36922 AN XY: 74310

African (AFR) AF: 0.646 AC: 26793 AN: 41470

American (AMR) AF: 0.374 AC: 5705 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.531 AC: 1840 AN: 3466

East Asian (EAS) AF: 0.320 AC: 1656 AN: 5170

South Asian (SAS) AF: 0.486 AC: 2345 AN: 4826

European-Finnish (FIN) AF: 0.434 AC: 4580 AN: 10554

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32197 AN: 67938

Other (OTH) AF: 0.503 AC: 1060 AN: 2108

Alfa AF: 0.488 Hom.: 3930

Bravo AF: 0.502

Asia WGS AF: 0.479 AC: 1668 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.27
DANN	Benign	0.52
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs7357405; hg19: chr8-79020700;