chr19-51223655-A-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000716537.1(ENSG00000268595):​n.244-28995T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,018 control chromosomes in the GnomAD database, including 14,671 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 0.43 ( 14671 hom., cov: 32)

Consequence

ENSG00000268595
ENST00000716537.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

Publications

12 publications found
Variant links:
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]

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-1.09).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD33XM_011527531.3 linkc.-51-1001A>C intron_variant Intron 5 of 12 XP_011525833.1
CD33XM_017027508.2 linkc.-51-1001A>C intron_variant Intron 5 of 12 XP_016882997.1
CD33XM_047439728.1 linkc.-51-1001A>C intron_variant Intron 4 of 11 XP_047295684.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ENSG00000268595ENST00000716537.1 linkn.244-28995T>G intron_variant Intron 2 of 4
ENSG00000268595ENST00000716538.1 linkn.244-28995T>G intron_variant Intron 2 of 4
ENSG00000268595ENST00000716539.1 linkn.246-28995T>G intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.428
AC:
65000
AN:
151900
Hom.:
14661
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.544
Gnomad AMI
AF:
0.506
Gnomad AMR
AF:
0.308
Gnomad ASJ
AF:
0.413
Gnomad EAS
AF:
0.0857
Gnomad SAS
AF:
0.256
Gnomad FIN
AF:
0.383
Gnomad MID
AF:
0.351
Gnomad NFE
AF:
0.430
Gnomad OTH
AF:
0.420
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.428
AC:
65044
AN:
152018
Hom.:
14671
Cov.:
32
AF XY:
0.418
AC XY:
31086
AN XY:
74312
show subpopulations
African (AFR)
AF:
0.544
AC:
22542
AN:
41428
American (AMR)
AF:
0.307
AC:
4697
AN:
15282
Ashkenazi Jewish (ASJ)
AF:
0.413
AC:
1434
AN:
3472
East Asian (EAS)
AF:
0.0847
AC:
439
AN:
5182
South Asian (SAS)
AF:
0.256
AC:
1232
AN:
4816
European-Finnish (FIN)
AF:
0.383
AC:
4041
AN:
10544
Middle Eastern (MID)
AF:
0.347
AC:
102
AN:
294
European-Non Finnish (NFE)
AF:
0.430
AC:
29211
AN:
67982
Other (OTH)
AF:
0.420
AC:
887
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.504
Heterozygous variant carriers
0
1836
3673
5509
7346
9182
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
596
1192
1788
2384
2980
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
0.417
Hom.:
8651
Bravo
AF:
0.429
Asia WGS
AF:
0.235
AC:
818
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-1.1
CADD
Benign
0.66
DANN
Benign
0.38
PhyloP100
-1.9

Splicing

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

Publications

Other links and lift over

dbSNP: rs1710398; hg19: chr19-51726911; API