rs10840606

Variant names:

• chr11-2213460-A-G
• rs10840606

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 0.13 in 151,528 control chromosomes in the GnomAD database, including 1,626 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 0.13 (1626 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.176 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: 0.130 AC: 19733 AN: 151412 Hom.: 1624 Cov.: 28

Gnomad AFR AF: 0.0350

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0650

Gnomad SAS AF: 0.154

Gnomad FIN AF: 0.214

Gnomad MID AF: 0.102

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.130 AC: 19731 AN: 151528 Hom.: 1626 Cov.: 28 AF XY: 0.130 AC XY: 9653 AN XY: 73984

Gnomad4 AFR AF: 0.0348

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0645

Gnomad4 SAS AF: 0.154

Gnomad4 FIN AF: 0.214

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.112

Alfa AF: 0.169 Hom.: 1567

Bravo AF: 0.117

Asia WGS AF: 0.117 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.82
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10840606; hg19: chr11-2234690;