rs10504906

Variant names:

• chr8-91406400-G-A
• rs10504906

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 0.0807 in 152,158 control chromosomes in the GnomAD database, including 635 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 0.081 (635 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.147 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: 0.0807 AC: 12267 AN: 152038 Hom.: 634 Cov.: 32

Gnomad AFR AF: 0.150

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0714

Gnomad ASJ AF: 0.0292

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.0456

Gnomad FIN AF: 0.0193

Gnomad MID AF: 0.0287

Gnomad NFE AF: 0.0593

Gnomad OTH AF: 0.0856

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

GnomAD4 genome AF: 0.0807 AC: 12280 AN: 152158 Hom.: 635 Cov.: 32 AF XY: 0.0767 AC XY: 5706 AN XY: 74402

Gnomad4 AFR AF: 0.150

Gnomad4 AMR AF: 0.0713

Gnomad4 ASJ AF: 0.0292

Gnomad4 EAS AF: 0.0314

Gnomad4 SAS AF: 0.0458

Gnomad4 FIN AF: 0.0193

Gnomad4 NFE AF: 0.0593

Gnomad4 OTH AF: 0.0843

Alfa AF: 0.0633 Hom.: 178

Bravo AF: 0.0887

Asia WGS AF: 0.0500 AC: 174 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	3.4
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10504906; hg19: chr8-92418628;