11-86118825-T-C

Variant names:

• chr11-86118825-T-C
• rs4944558

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.164 in 152,234 control chromosomes in the GnomAD database, including 2,390 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 0.16 (2390 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.838
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.42).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24887 AN: 152116 Hom.: 2390 Cov.: 32

Gnomad AFR AF: 0.0591

Gnomad AMI AF: 0.135

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.177

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.168

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.164 AC: 24909 AN: 152234 Hom.: 2390 Cov.: 32 AF XY: 0.163 AC XY: 12129 AN XY: 74428

African (AFR) AF: 0.0594 AC: 2470 AN: 41548

American (AMR) AF: 0.190 AC: 2911 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.177 AC: 613 AN: 3470

East Asian (EAS) AF: 0.375 AC: 1946 AN: 5186

South Asian (SAS) AF: 0.195 AC: 938 AN: 4822

European-Finnish (FIN) AF: 0.168 AC: 1779 AN: 10590

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.202 AC: 13712 AN: 68012

Other (OTH) AF: 0.170 AC: 360 AN: 2112

Alfa AF: 0.192 Hom.: 1786

Bravo AF: 0.160

Asia WGS AF: 0.284 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.42
CADD	Benign	15
DANN	Benign	0.90
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs4944558; hg19: chr11-85829867;