19-35346820-A-ACGCACACACACACACACACGCACGCACACACACACACACACGCACG

Variant names:

• chr19-35346820-A-ACGCACACACACACACACACGCACGCACACACACACACACACGCACG
• rs34472317
• NM_001771.4:c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001771.4(CD22):​c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000133 in 149,954 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.000013 (0 hom., cov: 31)
• Consequence: CD22 NM_001771.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.174
• Publications: 2 publications found

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]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001771.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	NM_001771.4	MANE Select	c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 14 of 14	NP_001762.2	P20273-1
	CD22	NM_001185099.2		c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 13 of 13	NP_001172028.1	P20273-3
	CD22	NM_001185100.2		c.*293_*294insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 13 of 13	NP_001172029.1	P20273-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	ENST00000085219.10	TSL:1 MANE Select	c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 14 of 14	ENSP00000085219.4	P20273-1
	CD22	ENST00000536635.6	TSL:1	c.*124_*125insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 13 of 13	ENSP00000442279.1	P20273-3
	CD22	ENST00000544992.6	TSL:1	c.*293_*294insGCACACACACACACACACGCACGCACACACACACACACACGCACGC		3_prime_UTR	Exon 13 of 13	ENSP00000441237.1	P20273-4

Frequencies

GnomAD3 genomes AF: 0.0000133 AC: 2 AN: 149954 Hom.: 0 Cov.: 31

Gnomad AFR AF: 0.0000489

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 9

GnomAD4 genome AF: 0.0000133 AC: 2 AN: 149954 Hom.: 0 Cov.: 31 AF XY: 0.0000137 AC XY: 1 AN XY: 73150

African (AFR) AF: 0.0000489 AC: 2 AN: 40892

American (AMR) AF: 0.00 AC: 0 AN: 15104

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3436

East Asian (EAS) AF: 0.00 AC: 0 AN: 5138

South Asian (SAS) AF: 0.00 AC: 0 AN: 4768

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10206

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67132

Other (OTH) AF: 0.00 AC: 0 AN: 2054

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

Other links and lift over

dbSNP: rs34472317; hg19: chr19-35837723;