rs11193438

chr10-107445944-G-A

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 0.15 in 151,960 control chromosomes in the GnomAD database, including 1,879 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 0.15 (1879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.630

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.216 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: 0.150 AC: 22735 AN: 151844 Hom.: 1875 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.0946

Gnomad ASJ AF: 0.0689

Gnomad EAS AF: 0.00444

Gnomad SAS AF: 0.0496

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.150 AC: 22749 AN: 151960 Hom.: 1879 Cov.: 32 AF XY: 0.148 AC XY: 10969 AN XY: 74272

Gnomad4 AFR AF: 0.219

Gnomad4 AMR AF: 0.0943

Gnomad4 ASJ AF: 0.0689

Gnomad4 EAS AF: 0.00445

Gnomad4 SAS AF: 0.0501

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.128

Alfa AF: 0.149 Hom.: 243

Bravo AF: 0.146

Asia WGS AF: 0.0430 AC: 151 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.60
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11193438; hg19: chr10-109205702;