rs3088063
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001771.4(CD22):c.*476C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0849 in 155,996 control chromosomes in the GnomAD database, including 668 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 0.085 ( 642 hom., cov: 32)
Exomes 𝑓: 0.072 ( 26 hom. )
Consequence
CD22
NM_001771.4 3_prime_UTR
NM_001771.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0380
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]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.209 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD22 | NM_001771.4 | c.*476C>T | 3_prime_UTR_variant | 14/14 | ENST00000085219.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD22 | ENST00000085219.10 | c.*476C>T | 3_prime_UTR_variant | 14/14 | 1 | NM_001771.4 | P2 | ||
CD22 | ENST00000536635.6 | c.*476C>T | 3_prime_UTR_variant | 13/13 | 1 | ||||
CD22 | ENST00000341773.10 | c.*476C>T | 3_prime_UTR_variant | 12/12 | 5 | ||||
CD22 | ENST00000601769.5 | c.*2325C>T | 3_prime_UTR_variant, NMD_transcript_variant | 14/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0850 AC: 12922AN: 152032Hom.: 630 Cov.: 32
GnomAD3 genomes
?
AF:
AC:
12922
AN:
152032
Hom.:
Cov.:
32
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0718 AC: 276AN: 3844Hom.: 26 Cov.: 0 AF XY: 0.0864 AC XY: 181AN XY: 2094
GnomAD4 exome
AF:
AC:
276
AN:
3844
Hom.:
Cov.:
0
AF XY:
AC XY:
181
AN XY:
2094
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.0852 AC: 12966AN: 152152Hom.: 642 Cov.: 32 AF XY: 0.0873 AC XY: 6495AN XY: 74378
GnomAD4 genome
?
AF:
AC:
12966
AN:
152152
Hom.:
Cov.:
32
AF XY:
AC XY:
6495
AN XY:
74378
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
716
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at