11-2180108-C-T

Variant names:

• chr11-2180108-C-T
• rs11564709

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 0.0626 in 152,220 control chromosomes in the GnomAD database, including 414 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 0.063 (414 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0925 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: 0.0627 AC: 9530 AN: 152104 Hom.: 414 Cov.: 33

Gnomad AFR AF: 0.0151

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.0467

Gnomad ASJ AF: 0.0772

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0939

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0944

Gnomad OTH AF: 0.0493

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

GnomAD4 genome AF: 0.0626 AC: 9531 AN: 152220 Hom.: 414 Cov.: 33 AF XY: 0.0617 AC XY: 4590 AN XY: 74428

Gnomad4 AFR AF: 0.0151

Gnomad4 AMR AF: 0.0466

Gnomad4 ASJ AF: 0.0772

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.0541

Gnomad4 FIN AF: 0.0939

Gnomad4 NFE AF: 0.0944

Gnomad4 OTH AF: 0.0488

Alfa AF: 0.0627 Hom.: 130

Bravo AF: 0.0564

Asia WGS AF: 0.0250 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.29
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11564709; hg19: chr11-2201338; COSMIC: COSV51398906;