rs11239832

chr10-42923919-C-Achr10-42923919-C-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 0.205 in 152,028 control chromosomes in the GnomAD database, including 3,840 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 0.21 (3840 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.55

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31132 AN: 151910 Hom.: 3823 Cov.: 33

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.246

Gnomad ASJ AF: 0.162

Gnomad EAS AF: 0.211

Gnomad SAS AF: 0.219

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.124

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.205 AC: 31196 AN: 152028 Hom.: 3840 Cov.: 33 AF XY: 0.209 AC XY: 15517 AN XY: 74292

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.162

Gnomad4 EAS AF: 0.211

Gnomad4 SAS AF: 0.218

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.124

Gnomad4 OTH AF: 0.212

Alfa AF: 0.111 Hom.: 253

Bravo AF: 0.220

Asia WGS AF: 0.228 AC: 795 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.055
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11239832; hg19: chr10-43419367;