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. The variant received -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
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.168 AC: 6975 AN: 41470

American (AMR) AF: 0.599 AC: 9152 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1885 AN: 3460

East Asian (EAS) AF: 0.636 AC: 3285 AN: 5164

South Asian (SAS) AF: 0.318 AC: 1534 AN: 4826

European-Finnish (FIN) AF: 0.605 AC: 6387 AN: 10554

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36482 AN: 67972

Other (OTH) AF: 0.484 AC: 1023 AN: 2112

Alfa AF: 0.512 Hom.: 34754

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
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs10886596; hg19: chr10-121865347;