chr8-58464798-G-A

Variant names:

• chr8-58464798-G-A
• rs6471717

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 0.703 in 151,986 control chromosomes in the GnomAD database, including 37,783 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 0.70 (37783 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 11 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 (EAS) allele frequency at 95% confidence interval = 0.773 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: 0.703 AC: 106694 AN: 151866 Hom.: 37731 Cov.: 31

Gnomad AFR AF: 0.780

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.764

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.781

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.603

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.654

Gnomad OTH AF: 0.701

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

GnomAD4 genome AF: 0.703 AC: 106804 AN: 151986 Hom.: 37783 Cov.: 31 AF XY: 0.701 AC XY: 52112 AN XY: 74298

African (AFR) AF: 0.780 AC: 32337 AN: 41474

American (AMR) AF: 0.764 AC: 11675 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3468

East Asian (EAS) AF: 0.781 AC: 4033 AN: 5164

South Asian (SAS) AF: 0.675 AC: 3249 AN: 4810

European-Finnish (FIN) AF: 0.603 AC: 6337 AN: 10504

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.654 AC: 44483 AN: 67974

Other (OTH) AF: 0.705 AC: 1484 AN: 2106

Alfa AF: 0.676 Hom.: 5287

Bravo AF: 0.720

Asia WGS AF: 0.730 AC: 2535 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.19
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs6471717; hg19: chr8-59377357;