rs11187146

Variant names:

• chr10-92718598-G-C
• rs11187146

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 0.148 in 151,802 control chromosomes in the GnomAD database, including 3,050 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 (3050 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.732
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.677 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: 0.148 AC: 22471 AN: 151684 Hom.: 3051 Cov.: 31

Gnomad AFR AF: 0.0316

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.171

Gnomad EAS AF: 0.696

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.208

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.148 AC: 22477 AN: 151802 Hom.: 3050 Cov.: 31 AF XY: 0.159 AC XY: 11808 AN XY: 74130

African (AFR) AF: 0.0315 AC: 1304 AN: 41434

American (AMR) AF: 0.245 AC: 3711 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.171 AC: 592 AN: 3470

East Asian (EAS) AF: 0.696 AC: 3582 AN: 5148

South Asian (SAS) AF: 0.369 AC: 1777 AN: 4812

European-Finnish (FIN) AF: 0.208 AC: 2187 AN: 10500

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8917 AN: 67952

Other (OTH) AF: 0.158 AC: 333 AN: 2104

Alfa AF: 0.134 Hom.: 279

Bravo AF: 0.149

Asia WGS AF: 0.467 AC: 1620 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	11
DANN	Benign	0.67
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs11187146; hg19: chr10-94478355;