8-58505225-A-G

Variant names:

• chr8-58505225-A-G
• rs13251096

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 0.527 in 152,068 control chromosomes in the GnomAD database, including 21,899 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 0.53 (21899 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.635 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: 0.527 AC: 80093 AN: 151950 Hom.: 21890 Cov.: 33

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.567

Gnomad AMR AF: 0.645

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.393

Gnomad SAS AF: 0.517

Gnomad FIN AF: 0.554

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.592

Gnomad OTH AF: 0.551

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

GnomAD4 genome AF: 0.527 AC: 80121 AN: 152068 Hom.: 21899 Cov.: 33 AF XY: 0.526 AC XY: 39132 AN XY: 74328

Gnomad4 AFR AF: 0.378

Gnomad4 AMR AF: 0.646

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.393

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.554

Gnomad4 NFE AF: 0.592

Gnomad4 OTH AF: 0.551

Alfa AF: 0.511 Hom.: 3270

Bravo AF: 0.530

Asia WGS AF: 0.458 AC: 1594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.056
DANN	Benign	0.54

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13251096; hg19: chr8-59417784;