rs10840002

Variant names:

• chr11-8221479-A-G
• rs10840002

Your query was ambiguous. Multiple possible variants found:

• chr11-8221479-A-G
• chr11-8221479-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 0.496 in 151,966 control chromosomes in the GnomAD database, including 21,186 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 0.50 (21186 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.651

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.627 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: 0.497 AC: 75434 AN: 151848 Hom.: 21189 Cov.: 31

Gnomad AFR AF: 0.214

Gnomad AMI AF: 0.609

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.557

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.522

Gnomad FIN AF: 0.585

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.632

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.496 AC: 75446 AN: 151966 Hom.: 21186 Cov.: 31 AF XY: 0.497 AC XY: 36882 AN XY: 74262

Gnomad4 AFR AF: 0.214

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.557

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.521

Gnomad4 FIN AF: 0.585

Gnomad4 NFE AF: 0.632

Gnomad4 OTH AF: 0.513

Alfa AF: 0.605 Hom.: 38114

Bravo AF: 0.484

Asia WGS AF: 0.447 AC: 1556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10840002; hg19: chr11-8243026;