rs1803254

Positions:

• chr19-51239889-G-C
• chr19-51239889-G-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001772.4(CD33):​c.*201G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 433,648 control chromosomes in the GnomAD database, including 5,573 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.16 (3114 hom., cov: 32)
  • Exomes 𝑓: 0.10 (2459 hom.)
• Consequence: CD33 NM_001772.4 3_prime_UTR
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.152

Genes affected

CD33 (HGNC:1659): (CD33 molecule) Enables protein phosphatase binding activity and sialic acid binding activity. Involved in several processes, including negative regulation of cytokine production; negative regulation of monocyte activation; and positive regulation of protein tyrosine phosphatase activity. Located in several cellular components, including Golgi apparatus; external side of plasma membrane; and peroxisome. [provided by Alliance of Genome Resources, Apr 2022]

CD33 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 19-51239889-G-C is Benign according to our data. Variant chr19-51239889-G-C is described in ClinVar as [Benign]. Clinvar id is 1282621.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD33	NM_001772.4	c.*201G>C		3_prime_UTR_variant	7/7	ENST00000262262.5	NP_001763.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD33	ENST00000262262.5	c.*201G>C		3_prime_UTR_variant	7/7	1	NM_001772.4	ENSP00000262262.3

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24626 AN: 152010 Hom.: 3101 Cov.: 32

Gnomad AFR AF: 0.277

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.326

Gnomad ASJ AF: 0.0660

Gnomad EAS AF: 0.321

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.0578

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0709

Gnomad OTH AF: 0.147

GnomAD4 exome AF: 0.104 AC: 29347 AN: 281518 Hom.: 2459 Cov.: 4 AF XY: 0.102 AC XY: 14816 AN XY: 145642

Gnomad4 AFR exome AF: 0.269

Gnomad4 AMR exome AF: 0.385

Gnomad4 ASJ exome AF: 0.0739

Gnomad4 EAS exome AF: 0.277

Gnomad4 SAS exome AF: 0.0951

Gnomad4 FIN exome AF: 0.0594

Gnomad4 NFE exome AF: 0.0704

Gnomad4 OTH exome AF: 0.120

GnomAD4 genome AF: 0.162 AC: 24687 AN: 152130 Hom.: 3114 Cov.: 32 AF XY: 0.164 AC XY: 12185 AN XY: 74382

Gnomad4 AFR AF: 0.277

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.0660

Gnomad4 EAS AF: 0.321

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0578

Gnomad4 NFE AF: 0.0709

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0495 Hom.: 48

Bravo AF: 0.190

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 19, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.7
DANN	Benign	0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1803254; hg19: chr19-51743144; COSMIC: COSV51803488; COSMIC: COSV51803488;