rs10888205

Positions:

• chr10-47172804-C-T

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 0.19 in 152,108 control chromosomes in the GnomAD database, including 3,536 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 0.19 (3536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16

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 (SAS) allele frequency at 95% confidence interval = 0.374 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.190 AC: 28892 AN: 151990 Hom.: 3538 Cov.: 32

Gnomad AFR AF: 0.0484

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.245

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.190 AC: 28885 AN: 152108 Hom.: 3536 Cov.: 32 AF XY: 0.194 AC XY: 14454 AN XY: 74330

Gnomad4 AFR AF: 0.0483

Gnomad4 AMR AF: 0.193

Gnomad4 ASJ AF: 0.245

Gnomad4 EAS AF: 0.149

Gnomad4 SAS AF: 0.389

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.241

Gnomad4 OTH AF: 0.215

Alfa AF: 0.234 Hom.: 4931

Bravo AF: 0.170

Asia WGS AF: 0.290 AC: 1009 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	0.60
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10888205; hg19: chr10-48566558;