rs11239832

Variant names:

• chr10-42923919-C-A
• rs11239832

Your query was ambiguous. Multiple possible variants found:

• chr10-42923919-C-A
• chr10-42923919-C-T

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 0.205 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.336 AC: 13929 AN: 41426

American (AMR) AF: 0.247 AC: 3768 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.162 AC: 561 AN: 3470

East Asian (EAS) AF: 0.211 AC: 1090 AN: 5168

South Asian (SAS) AF: 0.218 AC: 1049 AN: 4814

European-Finnish (FIN) AF: 0.168 AC: 1774 AN: 10558

Middle Eastern (MID) AF: 0.201 AC: 59 AN: 294

European-Non Finnish (NFE) AF: 0.124 AC: 8443 AN: 67996

Other (OTH) AF: 0.212 AC: 449 AN: 2116

Alfa AF: 0.119 Hom.: 293

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
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11239832; hg19: chr10-43419367;