11-119824741-T-C

Variant names:

• chr11-119824741-T-C
• rs525914

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 0.787 in 152,158 control chromosomes in the GnomAD database, including 47,514 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 0.79 (47514 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.64).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.845 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: 0.787 AC: 119616 AN: 152040 Hom.: 47466 Cov.: 33

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.857

Gnomad ASJ AF: 0.809

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.738

Gnomad FIN AF: 0.869

Gnomad MID AF: 0.778

Gnomad NFE AF: 0.819

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.787 AC: 119721 AN: 152158 Hom.: 47514 Cov.: 33 AF XY: 0.791 AC XY: 58830 AN XY: 74400

Gnomad4 AFR AF: 0.688

Gnomad4 AMR AF: 0.857

Gnomad4 ASJ AF: 0.809

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.739

Gnomad4 FIN AF: 0.869

Gnomad4 NFE AF: 0.819

Gnomad4 OTH AF: 0.793

Alfa AF: 0.806 Hom.: 7568

Bravo AF: 0.781

Asia WGS AF: 0.761 AC: 2644 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.64
CADD	Benign	14
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs525914; hg19: chr11-119695450; COSMIC: COSV73205669;