chr8-58464798-G-A

Position:

• chr8-58464798-G-A

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.780

Gnomad4 AMR AF: 0.764

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.781

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.603

Gnomad4 NFE AF: 0.654

Gnomad4 OTH AF: 0.705

Alfa AF: 0.673 Hom.: 5054

Bravo AF: 0.720

Asia WGS AF: 0.730 AC: 2535 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6471717; hg19: chr8-59377357;