rs10840606

Positions:

• chr11-2213460-A-G

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;