11-2212344-A-G

Variant names:

• chr11-2212344-A-G
• rs7127900

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 0.747 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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.741

Gnomad4 ASJ AF: 0.732

Gnomad4 EAS AF: 0.892

Gnomad4 SAS AF: 0.764

Gnomad4 FIN AF: 0.739

Gnomad4 NFE AF: 0.809

Gnomad4 OTH AF: 0.787

Alfa AF: 0.798 Hom.: 66110

Bravo AF: 0.741

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7127900; hg19: chr11-2233574;