11-73183803-T-C

Position:

• chr11-73183803-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 0.859 in 152,230 control chromosomes in the GnomAD database, including 57,351 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 0.86 (57351 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.239

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.946 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: 0.860 AC: 130746 AN: 152112 Hom.: 57337 Cov.: 33

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.958

Gnomad AMR AF: 0.902

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.783

Gnomad SAS AF: 0.916

Gnomad FIN AF: 0.913

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.953

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.859 AC: 130803 AN: 152230 Hom.: 57351 Cov.: 33 AF XY: 0.860 AC XY: 63996 AN XY: 74434

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.902

Gnomad4 ASJ AF: 0.921

Gnomad4 EAS AF: 0.784

Gnomad4 SAS AF: 0.916

Gnomad4 FIN AF: 0.913

Gnomad4 NFE AF: 0.953

Gnomad4 OTH AF: 0.886

Alfa AF: 0.893 Hom.: 7621

Bravo AF: 0.850

Asia WGS AF: 0.821 AC: 2856 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.2
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1791933; hg19: chr11-72894848;