rs10886596

Variant names:

• chr10-120105835-G-A
• rs10886596

Your query was ambiguous. Multiple possible variants found:

• chr10-120105835-G-A
• chr10-120105835-G-C

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 0.444 in 152,030 control chromosomes in the GnomAD database, including 17,439 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 0.44 (17439 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.618 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: 0.444 AC: 67430 AN: 151912 Hom.: 17433 Cov.: 32

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.627

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.319

Gnomad FIN AF: 0.605

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.444 AC: 67436 AN: 152030 Hom.: 17439 Cov.: 32 AF XY: 0.452 AC XY: 33543 AN XY: 74280

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.318

Gnomad4 FIN AF: 0.605

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.484

Alfa AF: 0.523 Hom.: 28092

Bravo AF: 0.436

Asia WGS AF: 0.475 AC: 1650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	14
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10886596; hg19: chr10-121865347;