rs10902845

Variant names:

• chr10-122923791-T-C
• rs10902845

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 0.0329 in 152,280 control chromosomes in the GnomAD database, including 316 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 0.033 (316 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 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: 0.0329 AC: 5000 AN: 152162 Hom.: 311 Cov.: 32

Gnomad AFR AF: 0.00649

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.00720

Gnomad EAS AF: 0.213

Gnomad SAS AF: 0.0244

Gnomad FIN AF: 0.0142

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0186

Gnomad OTH AF: 0.0354

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

GnomAD4 genome AF: 0.0329 AC: 5005 AN: 152280 Hom.: 316 Cov.: 32 AF XY: 0.0356 AC XY: 2651 AN XY: 74454

Gnomad4 AFR AF: 0.00647

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.00720

Gnomad4 EAS AF: 0.212

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.0142

Gnomad4 NFE AF: 0.0186

Gnomad4 OTH AF: 0.0350

Alfa AF: 0.0272 Hom.: 15

Bravo AF: 0.0446

Asia WGS AF: 0.0950 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10902845; hg19: chr10-124683307;