rs16970255

Variant names:

• chr19-35346943-C-A
• rs16970255
• NM_001771.4:c.*246C>A

Your query was ambiguous. Multiple possible variants found:

• chr19-35346943-C-A
• chr19-35346943-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001771.4(CD22):​c.*246C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000341 in 292,836 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0000034 (0 hom.)
• Consequence: CD22 NM_001771.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 0 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	NM_001771.4	MANE Select	c.*246C>A		3_prime_UTR	Exon 14 of 14	NP_001762.2
	CD22	NM_001185099.2		c.*246C>A		3_prime_UTR	Exon 13 of 13	NP_001172028.1
	CD22	NM_001185100.2		c.*415C>A		3_prime_UTR	Exon 13 of 13	NP_001172029.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD22	ENST00000085219.10	TSL:1 MANE Select	c.*246C>A		3_prime_UTR	Exon 14 of 14	ENSP00000085219.4
	CD22	ENST00000536635.6	TSL:1	c.*246C>A		3_prime_UTR	Exon 13 of 13	ENSP00000442279.1
	CD22	ENST00000601769.5	TSL:2	n.*2095C>A		non_coding_transcript_exon	Exon 14 of 14	ENSP00000470193.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000341 AC: 1 AN: 292836 Hom.: 0 Cov.: 3 AF XY: 0.00 AC XY: 0 AN XY: 153282

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 7252

American (AMR) AF: 0.00 AC: 0 AN: 8996

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 9356

East Asian (EAS) AF: 0.00 AC: 0 AN: 18558

South Asian (SAS) AF: 0.00 AC: 0 AN: 28304

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 19070

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1362

European-Non Finnish (NFE) AF: 0.00000548 AC: 1 AN: 182416

Other (OTH) AF: 0.00 AC: 0 AN: 17522

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.95
DANN	Benign	0.67
PhyloP100		-1.2

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs16970255; hg19: chr19-35837846;