11-2212344-A-G

Variant names:

• chr11-2212344-A-G
• rs7127900

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 0.747 in 151,900 control chromosomes in the GnomAD database, including 42,945 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 0.75 (42945 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 120 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113441 AN: 151782 Hom.: 42932 Cov.: 32

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.732

Gnomad EAS AF: 0.891

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.739

Gnomad MID AF: 0.818

Gnomad NFE AF: 0.809

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.747 AC: 113503 AN: 151900 Hom.: 42945 Cov.: 32 AF XY: 0.746 AC XY: 55392 AN XY: 74206

African (AFR) AF: 0.629 AC: 26022 AN: 41374

American (AMR) AF: 0.741 AC: 11320 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.732 AC: 2543 AN: 3472

East Asian (EAS) AF: 0.892 AC: 4577 AN: 5134

South Asian (SAS) AF: 0.764 AC: 3692 AN: 4830

European-Finnish (FIN) AF: 0.739 AC: 7773 AN: 10522

Middle Eastern (MID) AF: 0.822 AC: 240 AN: 292

European-Non Finnish (NFE) AF: 0.809 AC: 54980 AN: 67970

Other (OTH) AF: 0.787 AC: 1663 AN: 2114

Alfa AF: 0.794 Hom.: 91875

Bravo AF: 0.741

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.077
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs7127900; hg19: chr11-2233574;