chr11-45831095-T-C

Position:

• chr11-45831095-T-C

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 0.777 in 152,042 control chromosomes in the GnomAD database, including 47,331 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 0.78 (47331 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.873 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.777 AC: 118077 AN: 151924 Hom.: 47311 Cov.: 31

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.851

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.891

Gnomad EAS AF: 0.374

Gnomad SAS AF: 0.792

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.812

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.777 AC: 118146 AN: 152042 Hom.: 47331 Cov.: 31 AF XY: 0.775 AC XY: 57646 AN XY: 74348

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.891

Gnomad4 EAS AF: 0.373

Gnomad4 SAS AF: 0.790

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.879

Gnomad4 OTH AF: 0.781

Alfa AF: 0.854 Hom.: 73980

Bravo AF: 0.756

Asia WGS AF: 0.673 AC: 2343 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	0.68
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2090602; hg19: chr11-45852646;