chr11-23496859-A-G

Position:

• chr11-23496859-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 0.843 in 152,182 control chromosomes in the GnomAD database, including 54,109 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 0.84 (54109 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

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 (EAS) allele frequency at 95% confidence interval = 0.975 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: 0.843 AC: 128213 AN: 152064 Hom.: 54051 Cov.: 32

Gnomad AFR AF: 0.864

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.825

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.865

Gnomad FIN AF: 0.855

Gnomad MID AF: 0.756

Gnomad NFE AF: 0.826

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.843 AC: 128326 AN: 152182 Hom.: 54109 Cov.: 32 AF XY: 0.847 AC XY: 62985 AN XY: 74400

Gnomad4 AFR AF: 0.864

Gnomad4 AMR AF: 0.825

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.865

Gnomad4 FIN AF: 0.855

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.809

Alfa AF: 0.827 Hom.: 48050

Bravo AF: 0.843

Asia WGS AF: 0.909 AC: 3159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
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: rs1350948; hg19: chr11-23518405;