rs11239011

chr10-44361515-G-Achr10-44361515-G-C

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 0.0581 in 152,312 control chromosomes in the GnomAD database, including 297 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 0.058 (297 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.145

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0911 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: 0.0580 AC: 8830 AN: 152194 Hom.: 296 Cov.: 33

Gnomad AFR AF: 0.0349

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0949

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.0431

Gnomad SAS AF: 0.0718

Gnomad FIN AF: 0.0472

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0673

Gnomad OTH AF: 0.0526

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

GnomAD4 genome AF: 0.0581 AC: 8842 AN: 152312 Hom.: 297 Cov.: 33 AF XY: 0.0578 AC XY: 4306 AN XY: 74486

Gnomad4 AFR AF: 0.0349

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.0432

Gnomad4 SAS AF: 0.0727

Gnomad4 FIN AF: 0.0472

Gnomad4 NFE AF: 0.0673

Gnomad4 OTH AF: 0.0516

Alfa AF: 0.0440 Hom.: 42

Bravo AF: 0.0605

Asia WGS AF: 0.0640 AC: 223 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	1.9
Dann	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11239011; hg19: chr10-44856963;