rs10505407

Variant names:

• chr8-121498201-A-G
• rs10505407

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 0.0718 in 152,204 control chromosomes in the GnomAD database, including 748 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 0.072 (748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.494

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.173 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: 0.0716 AC: 10892 AN: 152088 Hom.: 742 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0526

Gnomad AMR AF: 0.0705

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.0343

Gnomad SAS AF: 0.0283

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.0669

Gnomad NFE AF: 0.0265

Gnomad OTH AF: 0.0630

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

GnomAD4 genome AF: 0.0718 AC: 10925 AN: 152204 Hom.: 748 Cov.: 32 AF XY: 0.0715 AC XY: 5322 AN XY: 74436

Gnomad4 AFR AF: 0.176

Gnomad4 AMR AF: 0.0703

Gnomad4 ASJ AF: 0.0521

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0282

Gnomad4 FIN AF: 0.00490

Gnomad4 NFE AF: 0.0265

Gnomad4 OTH AF: 0.0619

Alfa AF: 0.0388 Hom.: 125

Bravo AF: 0.0811

Asia WGS AF: 0.0650 AC: 226 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.47
DANN	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10505407; hg19: chr8-122510441;