rs10840606

Variant names:

• chr11-2213460-A-G
• rs10840606

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 0.13 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
• Publications: 23 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.0348 AC: 1440 AN: 41342

American (AMR) AF: 0.112 AC: 1704 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 729 AN: 3468

East Asian (EAS) AF: 0.0645 AC: 333 AN: 5160

South Asian (SAS) AF: 0.154 AC: 739 AN: 4796

European-Finnish (FIN) AF: 0.214 AC: 2227 AN: 10414

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.178 AC: 12083 AN: 67822

Other (OTH) AF: 0.112 AC: 235 AN: 2102

Alfa AF: 0.168 Hom.: 2388

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
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10840606; hg19: chr11-2234690;