11-2289922-T-G

Variant names:

• chr11-2289922-T-G
• rs7944004

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 0.473 in 151,976 control chromosomes in the GnomAD database, including 17,365 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 0.47 (17365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0670
• Publications: 31 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.507 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.473 AC: 71809 AN: 151858 Hom.: 17359 Cov.: 32

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.469

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.196

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.473 AC: 71843 AN: 151976 Hom.: 17365 Cov.: 32 AF XY: 0.472 AC XY: 35046 AN XY: 74268

African (AFR) AF: 0.460 AC: 19073 AN: 41434

American (AMR) AF: 0.413 AC: 6308 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1369 AN: 3468

East Asian (EAS) AF: 0.196 AC: 1012 AN: 5166

South Asian (SAS) AF: 0.497 AC: 2391 AN: 4812

European-Finnish (FIN) AF: 0.512 AC: 5408 AN: 10554

Middle Eastern (MID) AF: 0.462 AC: 135 AN: 292

European-Non Finnish (NFE) AF: 0.512 AC: 34769 AN: 67938

Other (OTH) AF: 0.450 AC: 951 AN: 2112

Alfa AF: 0.489 Hom.: 63988

Bravo AF: 0.464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.067

Splicing

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

Other links and lift over

dbSNP: rs7944004; hg19: chr11-2311152;