rs11193438

Variant names:

• chr10-107445944-G-A
• rs11193438

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 0.15 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
• Publications: 1 publications found

ACMG classification

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.219 AC: 9086 AN: 41414

American (AMR) AF: 0.0943 AC: 1440 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0689 AC: 239 AN: 3470

East Asian (EAS) AF: 0.00445 AC: 23 AN: 5168

South Asian (SAS) AF: 0.0501 AC: 241 AN: 4814

European-Finnish (FIN) AF: 0.163 AC: 1721 AN: 10534

Middle Eastern (MID) AF: 0.103 AC: 30 AN: 292

European-Non Finnish (NFE) AF: 0.141 AC: 9558 AN: 67980

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.151 Hom.: 257

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
PhyloP100		-0.63

Splicing

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

Other links and lift over

dbSNP: rs11193438; hg19: chr10-109205702;