11-20232053-A-G

Position:

• chr11-20232053-A-G

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 0.685 in 151,658 control chromosomes in the GnomAD database, including 36,443 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 0.69 (36443 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.20

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.685 AC: 103879 AN: 151540 Hom.: 36428 Cov.: 30

Gnomad AFR AF: 0.581

Gnomad AMI AF: 0.796

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.850

Gnomad FIN AF: 0.764

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.747

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.685 AC: 103930 AN: 151658 Hom.: 36443 Cov.: 30 AF XY: 0.689 AC XY: 51013 AN XY: 74088

Gnomad4 AFR AF: 0.581

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.677

Gnomad4 EAS AF: 0.449

Gnomad4 SAS AF: 0.849

Gnomad4 FIN AF: 0.764

Gnomad4 NFE AF: 0.747

Gnomad4 OTH AF: 0.686

Alfa AF: 0.728 Hom.: 62915

Bravo AF: 0.665

Asia WGS AF: 0.685 AC: 2378 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	13
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1353649; hg19: chr11-20253599;