rs10885390

chr10-112881038-T-A

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 0.294 in 152,098 control chromosomes in the GnomAD database, including 6,994 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 0.29 (6994 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.438

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.295 AC: 44766 AN: 151980 Hom.: 6990 Cov.: 32

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.243

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.00211

Gnomad SAS AF: 0.198

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.301

Gnomad OTH AF: 0.313

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

GnomAD4 genome AF: 0.294 AC: 44790 AN: 152098 Hom.: 6994 Cov.: 32 AF XY: 0.292 AC XY: 21712 AN XY: 74350

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.243

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.00212

Gnomad4 SAS AF: 0.198

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.301

Gnomad4 OTH AF: 0.310

Alfa AF: 0.293 Hom.: 844

Bravo AF: 0.291

Asia WGS AF: 0.0940 AC: 330 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.4
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10885390; hg19: chr10-114640797;