rs10504878

chr8-89394928-A-G

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 0.0128 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.00787

Gnomad4 AMR AF: 0.00512

Gnomad4 ASJ AF: 0.0372

Gnomad4 EAS AF: 0.128

Gnomad4 SAS AF: 0.0778

Gnomad4 FIN AF: 0.00122

Gnomad4 NFE AF: 0.00462

Gnomad4 OTH AF: 0.0104

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504878; hg19: chr8-90407157;