rs10882165

Positions:

• chr10-93164567-A-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 0.386 in 151,900 control chromosomes in the GnomAD database, including 11,896 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 0.39 (11896 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.42 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: 0.387 AC: 58672 AN: 151780 Hom.: 11900 Cov.: 31

Gnomad AFR AF: 0.401

Gnomad AMI AF: 0.262

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.0187

Gnomad SAS AF: 0.305

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.435

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.386 AC: 58683 AN: 151900 Hom.: 11896 Cov.: 31 AF XY: 0.379 AC XY: 28163 AN XY: 74244

Gnomad4 AFR AF: 0.400

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.388

Gnomad4 EAS AF: 0.0186

Gnomad4 SAS AF: 0.304

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.424

Gnomad4 OTH AF: 0.391

Alfa AF: 0.419 Hom.: 1712

Bravo AF: 0.384

Asia WGS AF: 0.169 AC: 587 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.5
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10882165; hg19: chr10-94924324;