22-40646358-T-TATC

Variant names:

• chr22-40646358-T-TATC
• rs133052

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.82 (51601 hom., cov: 0)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.959 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: 0.817 AC: 123912 AN: 151626 Hom.: 51544 Cov.: 0

Gnomad AFR AF: 0.949

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.614

Gnomad ASJ AF: 0.821

Gnomad EAS AF: 0.982

Gnomad SAS AF: 0.842

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.894

Gnomad NFE AF: 0.773

Gnomad OTH AF: 0.797

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

GnomAD4 genome AF: 0.817 AC: 124023 AN: 151744 Hom.: 51601 Cov.: 0 AF XY: 0.817 AC XY: 60520 AN XY: 74118

African (AFR) AF: 0.949 AC: 39323 AN: 41440

American (AMR) AF: 0.614 AC: 9351 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.821 AC: 2841 AN: 3462

East Asian (EAS) AF: 0.982 AC: 5052 AN: 5144

South Asian (SAS) AF: 0.842 AC: 4058 AN: 4818

European-Finnish (FIN) AF: 0.802 AC: 8433 AN: 10510

Middle Eastern (MID) AF: 0.897 AC: 260 AN: 290

European-Non Finnish (NFE) AF: 0.773 AC: 52453 AN: 67842

Other (OTH) AF: 0.799 AC: 1680 AN: 2102

Alfa AF: 0.713 Hom.: 1476

Bravo AF: 0.803

Asia WGS AF: 0.889 AC: 3084 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.17

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs133052; hg19: chr22-41042362;