19-35346820-A-ACGCACG

Variant names:

• chr19-35346820-A-ACGCACG
• rs34472317
• NM_001771.4:c.*124_*125insGCACGC

Variant summary

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

The NM_001771.4(CD22):​c.*124_*125insGCACGC variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000141 in 426,206 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.000013 (0 hom., cov: 31)
  • Exomes 𝑓: 0.000014 (0 hom.)
• 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_*125insGCACGC		3_prime_UTR	Exon 14 of 14	NP_001762.2	P20273-1
	CD22	NM_001185099.2		c.*124_*125insGCACGC		3_prime_UTR	Exon 13 of 13	NP_001172028.1	P20273-3
	CD22	NM_001185100.2		c.*293_*294insGCACGC		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_*125insGCACGC		3_prime_UTR	Exon 14 of 14	ENSP00000085219.4	P20273-1
	CD22	ENST00000536635.6	TSL:1	c.*124_*125insGCACGC		3_prime_UTR	Exon 13 of 13	ENSP00000442279.1	P20273-3
	CD22	ENST00000544992.6	TSL:1	c.*293_*294insGCACGC		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: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000132

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 AF: 0.0000145 AC: 4 AN: 276152 Hom.: 0 Cov.: 9 AF XY: 0.0000213 AC XY: 3 AN XY: 141038

African (AFR) AF: 0.00 AC: 0 AN: 10494

American (AMR) AF: 0.000531 AC: 4 AN: 7534

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 5552

East Asian (EAS) AF: 0.00 AC: 0 AN: 12280

South Asian (SAS) AF: 0.00 AC: 0 AN: 25322

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 12572

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 998

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 187898

Other (OTH) AF: 0.00 AC: 0 AN: 13502

GnomAD4 genome AF: 0.0000133 AC: 2 AN: 150054 Hom.: 0 Cov.: 31 AF XY: 0.0000136 AC XY: 1 AN XY: 73266

African (AFR) AF: 0.00 AC: 0 AN: 41008

American (AMR) AF: 0.000132 AC: 2 AN: 15122

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5124

South Asian (SAS) AF: 0.00 AC: 0 AN: 4762

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

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67122

Other (OTH) AF: 0.00 AC: 0 AN: 2072

Alfa AF: 0.00 Hom.: 8

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;