chr8-58507859-G-A

Variant names:

• chr8-58507859-G-A
• rs1023649

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 0.538 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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.418 AC: 17243 AN: 41252

American (AMR) AF: 0.649 AC: 9872 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2118 AN: 3466

East Asian (EAS) AF: 0.392 AC: 2028 AN: 5170

South Asian (SAS) AF: 0.515 AC: 2476 AN: 4810

European-Finnish (FIN) AF: 0.555 AC: 5802 AN: 10450

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.592 AC: 40209 AN: 67914

Other (OTH) AF: 0.556 AC: 1170 AN: 2104

Alfa AF: 0.574 Hom.: 70636

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
PhyloP100		-0.35

Splicing

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

Other links and lift over

dbSNP: rs1023649; hg19: chr8-59420418;