11-20247844-A-G

Position:

• chr11-20247844-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.765 in 152,088 control chromosomes in the GnomAD database, including 45,179 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 0.76 (45179 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.72

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.892 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.20247844A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.765 AC: 116236 AN: 151970 Hom.: 45148 Cov.: 32

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.875

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.818

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.832

Gnomad OTH AF: 0.762

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

GnomAD4 genome AF: 0.765 AC: 116317 AN: 152088 Hom.: 45179 Cov.: 32 AF XY: 0.768 AC XY: 57066 AN XY: 74346

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.915

Gnomad4 FIN AF: 0.818

Gnomad4 NFE AF: 0.832

Gnomad4 OTH AF: 0.764

Alfa AF: 0.813 Hom.: 72511

Bravo AF: 0.749

Asia WGS AF: 0.780 AC: 2717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Benign	19
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1520896; hg19: chr11-20269390;