rs10504878

Variant names:

• chr8-89394928-A-G
• rs10504878

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 0.0128 in 152,110 control chromosomes in the GnomAD database, including 69 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 0.013 (69 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.12 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: 0.0128 AC: 1946 AN: 151992 Hom.: 69 Cov.: 32

Gnomad AFR AF: 0.00787

Gnomad AMI AF: 0.0307

Gnomad AMR AF: 0.00513

Gnomad ASJ AF: 0.0372

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.0771

Gnomad FIN AF: 0.00122

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00462

Gnomad OTH AF: 0.0101

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

GnomAD4 genome AF: 0.0128 AC: 1948 AN: 152110 Hom.: 69 Cov.: 32 AF XY: 0.0148 AC XY: 1097 AN XY: 74342

African (AFR) AF: 0.00787 AC: 327 AN: 41546

American (AMR) AF: 0.00512 AC: 78 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.0372 AC: 129 AN: 3464

East Asian (EAS) AF: 0.128 AC: 659 AN: 5146

South Asian (SAS) AF: 0.0778 AC: 375 AN: 4822

European-Finnish (FIN) AF: 0.00122 AC: 13 AN: 10628

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00462 AC: 314 AN: 67954

Other (OTH) AF: 0.0104 AC: 22 AN: 2110

Alfa AF: 0.00641 Hom.: 1

Bravo AF: 0.0128

Asia WGS AF: 0.0740 AC: 259 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.1
DANN	Benign	0.82
PhyloP100		0.44

Splicing

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

Other links and lift over

dbSNP: rs10504878; hg19: chr8-90407157;