11-23496859-A-G

Variant names:

• chr11-23496859-A-G
• rs1350948

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	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

African (AFR) AF: 0.864 AC: 35891 AN: 41532

American (AMR) AF: 0.825 AC: 12609 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3472

East Asian (EAS) AF: 0.997 AC: 5142 AN: 5156

South Asian (SAS) AF: 0.865 AC: 4171 AN: 4824

European-Finnish (FIN) AF: 0.855 AC: 9057 AN: 10596

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.826 AC: 56138 AN: 68002

Other (OTH) AF: 0.809 AC: 1706 AN: 2110

Alfa AF: 0.829 Hom.: 64328

Bravo AF: 0.843

Asia WGS AF: 0.909 AC: 3159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.70
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1350948; hg19: chr11-23518405;