11-19111865-G-C

Variant names:

• chr11-19111865-G-C
• rs11025015

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 0.0728 in 152,230 control chromosomes in the GnomAD database, including 725 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 0.073 (725 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.219

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.163 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: 0.0727 AC: 11065 AN: 152112 Hom.: 725 Cov.: 33

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.0691

Gnomad AMR AF: 0.0418

Gnomad ASJ AF: 0.0251

Gnomad EAS AF: 0.00327

Gnomad SAS AF: 0.0402

Gnomad FIN AF: 0.0271

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0401

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0728 AC: 11081 AN: 152230 Hom.: 725 Cov.: 33 AF XY: 0.0706 AC XY: 5251 AN XY: 74408

Gnomad4 AFR AF: 0.167

Gnomad4 AMR AF: 0.0417

Gnomad4 ASJ AF: 0.0251

Gnomad4 EAS AF: 0.00328

Gnomad4 SAS AF: 0.0411

Gnomad4 FIN AF: 0.0271

Gnomad4 NFE AF: 0.0401

Gnomad4 OTH AF: 0.0578

Alfa AF: 0.0142 Hom.: 4

Bravo AF: 0.0780

Asia WGS AF: 0.0260 AC: 90 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.3
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11025015; hg19: chr11-19133412;