rs34472317
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1
The NM_001771.4(CD22):c.*124_*125insGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0756 in 425,680 control chromosomes in the GnomAD database, including 1,486 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.084 ( 1081 hom., cov: 31)
Exomes 𝑓: 0.071 ( 405 hom. )
Consequence
CD22
NM_001771.4 3_prime_UTR
NM_001771.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.174
Genes affected
CD22 (HGNC:1643): (CD22 molecule) Predicted to enable CD4 receptor binding activity; protein phosphatase binding activity; and sialic acid binding activity. Involved in B cell activation; negative regulation of B cell receptor signaling pathway; and regulation of endocytosis. Located in early endosome and recycling endosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -8 ACMG points.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD22 | NM_001771.4 | c.*124_*125insGC | 3_prime_UTR_variant | 14/14 | ENST00000085219.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD22 | ENST00000085219.10 | c.*124_*125insGC | 3_prime_UTR_variant | 14/14 | 1 | NM_001771.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0833 AC: 12484AN: 149926Hom.: 1065 Cov.: 31
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GnomAD4 exome AF: 0.0713 AC: 19652AN: 275654Hom.: 405 Cov.: 9 AF XY: 0.0745 AC XY: 10486AN XY: 140776
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GnomAD4 genome ? AF: 0.0837 AC: 12550AN: 150026Hom.: 1081 Cov.: 31 AF XY: 0.0827 AC XY: 6060AN XY: 73250
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ClinVar
Not reported inComputational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at