rs10902845

Variant names:

• chr10-122923791-T-C
• rs10902845

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 0.0329 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.00647 AC: 269 AN: 41574

American (AMR) AF: 0.128 AC: 1965 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.00720 AC: 25 AN: 3470

East Asian (EAS) AF: 0.212 AC: 1097 AN: 5176

South Asian (SAS) AF: 0.0244 AC: 118 AN: 4830

European-Finnish (FIN) AF: 0.0142 AC: 151 AN: 10612

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0186 AC: 1267 AN: 68008

Other (OTH) AF: 0.0350 AC: 74 AN: 2112

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
PhyloP100		0.19

Splicing

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

Other links and lift over

dbSNP: rs10902845; hg19: chr10-124683307;