8-58507859-G-A

Position:

• chr8-58507859-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 0.538 in 151,574 control chromosomes in the GnomAD database, including 22,548 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 0.54 (22548 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.349

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.639 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: 0.539 AC: 81569 AN: 151456 Hom.: 22535 Cov.: 30

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.557

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

GnomAD4 genome AF: 0.538 AC: 81611 AN: 151574 Hom.: 22548 Cov.: 30 AF XY: 0.537 AC XY: 39755 AN XY: 74016

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.611

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.556

Alfa AF: 0.582 Hom.: 43690

Bravo AF: 0.542

Asia WGS AF: 0.462 AC: 1606 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.84
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023649; hg19: chr8-59420418;