rs11239809

Variant names:

• chr10-42888730-C-A
• rs11239809

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 0.192 in 152,166 control chromosomes in the GnomAD database, including 3,028 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 0.19 (3028 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.284
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.23 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: 0.192 AC: 29237 AN: 152046 Hom.: 3026 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.277

Gnomad AMR AF: 0.135

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0227

Gnomad SAS AF: 0.0739

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.137

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.177

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

GnomAD4 genome AF: 0.192 AC: 29255 AN: 152166 Hom.: 3028 Cov.: 32 AF XY: 0.186 AC XY: 13839 AN XY: 74404

African (AFR) AF: 0.175 AC: 7249 AN: 41506

American (AMR) AF: 0.135 AC: 2068 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 536 AN: 3472

East Asian (EAS) AF: 0.0230 AC: 119 AN: 5176

South Asian (SAS) AF: 0.0752 AC: 363 AN: 4826

European-Finnish (FIN) AF: 0.228 AC: 2415 AN: 10580

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15840 AN: 67992

Other (OTH) AF: 0.174 AC: 368 AN: 2112

Alfa AF: 0.205 Hom.: 598

Bravo AF: 0.186

Asia WGS AF: 0.0670 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.6
DANN	Benign	0.42
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11239809; hg19: chr10-43384178;