chr11-110870290-A-G

Variant names:

• chr11-110870290-A-G
• rs1469170

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 0.547 in 151,986 control chromosomes in the GnomAD database, including 25,003 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 0.55 (25003 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.758
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.675 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: 0.547 AC: 83141 AN: 151868 Hom.: 24988 Cov.: 32

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.668

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.680

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.547 AC: 83184 AN: 151986 Hom.: 25003 Cov.: 32 AF XY: 0.544 AC XY: 40424 AN XY: 74264

African (AFR) AF: 0.295 AC: 12214 AN: 41434

American (AMR) AF: 0.600 AC: 9166 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.668 AC: 2321 AN: 3472

East Asian (EAS) AF: 0.383 AC: 1974 AN: 5158

South Asian (SAS) AF: 0.550 AC: 2645 AN: 4812

European-Finnish (FIN) AF: 0.609 AC: 6420 AN: 10544

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.680 AC: 46243 AN: 67970

Other (OTH) AF: 0.589 AC: 1245 AN: 2114

Alfa AF: 0.631 Hom.: 50638

Bravo AF: 0.537

Asia WGS AF: 0.496 AC: 1727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.70
DANN	Benign	0.36
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs1469170; hg19: chr11-110741014;