8-58485902-G-A

Variant names:

• chr8-58485902-G-A
• rs10504255

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.745 in 152,144 control chromosomes in the GnomAD database, including 43,272 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 0.75 (43272 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.293
• Publications: 19 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.916 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: 0.745 AC: 113229 AN: 152026 Hom.: 43208 Cov.: 32

Gnomad AFR AF: 0.924

Gnomad AMI AF: 0.646

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.790

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.608

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.656

Gnomad OTH AF: 0.729

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

GnomAD4 genome AF: 0.745 AC: 113355 AN: 152144 Hom.: 43272 Cov.: 32 AF XY: 0.742 AC XY: 55184 AN XY: 74352

African (AFR) AF: 0.924 AC: 38378 AN: 41534

American (AMR) AF: 0.776 AC: 11870 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2407 AN: 3472

East Asian (EAS) AF: 0.791 AC: 4085 AN: 5164

South Asian (SAS) AF: 0.676 AC: 3255 AN: 4814

European-Finnish (FIN) AF: 0.608 AC: 6429 AN: 10566

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.656 AC: 44586 AN: 67986

Other (OTH) AF: 0.732 AC: 1541 AN: 2104

Alfa AF: 0.683 Hom.: 60419

Bravo AF: 0.766

Asia WGS AF: 0.742 AC: 2578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	12
DANN	Benign	0.79
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs10504255; hg19: chr8-59398461;