rs10886492

Variant names:

• chr10-119465964-G-A
• rs10886492

Your query was ambiguous. Multiple possible variants found:

• chr10-119465964-G-A
• chr10-119465964-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 0.293 in 152,076 control chromosomes in the GnomAD database, including 7,498 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 (7498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0710
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 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: 0.293 AC: 44550 AN: 151958 Hom.: 7494 Cov.: 32

Gnomad AFR AF: 0.131

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.318

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.293 AC: 44572 AN: 152076 Hom.: 7498 Cov.: 32 AF XY: 0.294 AC XY: 21818 AN XY: 74322

African (AFR) AF: 0.131 AC: 5432 AN: 41492

American (AMR) AF: 0.318 AC: 4855 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1666 AN: 3468

East Asian (EAS) AF: 0.271 AC: 1405 AN: 5176

South Asian (SAS) AF: 0.336 AC: 1621 AN: 4826

European-Finnish (FIN) AF: 0.360 AC: 3798 AN: 10552

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24805 AN: 67966

Other (OTH) AF: 0.325 AC: 686 AN: 2112

Alfa AF: 0.355 Hom.: 14740

Bravo AF: 0.283

Asia WGS AF: 0.270 AC: 942 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.48
PhyloP100		-0.071

Splicing

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

Other links and lift over

dbSNP: rs10886492; hg19: chr10-121225476;