chr8-58507952-C-A

Variant names:

• chr8-58507952-C-A
• rs1023651

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 0.539 in 151,780 control chromosomes in the GnomAD database, including 22,591 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 (22591 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.225

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81695 AN: 151662 Hom.: 22578 Cov.: 31

Gnomad AFR AF: 0.418

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.394

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.556

Gnomad MID AF: 0.585

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.555

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

GnomAD4 genome AF: 0.539 AC: 81737 AN: 151780 Hom.: 22591 Cov.: 31 AF XY: 0.537 AC XY: 39828 AN XY: 74136

Gnomad4 AFR AF: 0.418

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.394

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.556

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.555

Alfa AF: 0.407 Hom.: 1057

Bravo AF: 0.542

Asia WGS AF: 0.462 AC: 1607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.98
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1023651; hg19: chr8-59420511;