11-86118825-T-C

Variant names:

• chr11-86118825-T-C
• rs4944558

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.164 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

Gnomad4 AFR AF: 0.0594

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.177

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.168

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.170

Alfa AF: 0.192 Hom.: 1621

Bravo AF: 0.160

Asia WGS AF: 0.284 AC: 985 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4944558; hg19: chr11-85829867;