20-23084738-GTCC-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PM4_SupportingBP6

The NM_012072.4(CD93):​c.1452_1454delGGA​(p.Glu484del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000334 in 1,607,004 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (no stars).

Frequency

Genomes: 𝑓 0.00034 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00033 ( 0 hom. )

Consequence

CD93
NM_012072.4 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Likely benign no assertion criteria provided B:1

Conservation

PhyloP100: 0.249
Variant links:
Genes affected
CD93 (HGNC:15855): (CD93 molecule) The protein encoded by this gene is a cell-surface glycoprotein and type I membrane protein that was originally identified as a myeloid cell-specific marker. The encoded protein was once thought to be a receptor for C1q, but now is thought to instead be involved in intercellular adhesion and in the clearance of apoptotic cells. The intracellular cytoplasmic tail of this protein has been found to interact with moesin, a protein known to play a role in linking transmembrane proteins to the cytoskeleton and in the remodelling of the cytoskeleton. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_012072.4. Strenght limited to Supporting due to length of the change: 1aa.
BP6
Variant 20-23084738-GTCC-G is Benign according to our data. Variant chr20-23084738-GTCC-G is described in ClinVar as [Likely_benign]. Clinvar id is 3044385.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD93NM_012072.4 linkc.1452_1454delGGA p.Glu484del disruptive_inframe_deletion 1/2 ENST00000246006.5 NP_036204.2 Q9NPY3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD93ENST00000246006.5 linkc.1452_1454delGGA p.Glu484del disruptive_inframe_deletion 1/21 NM_012072.4 ENSP00000246006.4 Q9NPY3

Frequencies

GnomAD3 genomes
AF:
0.000342
AC:
52
AN:
152128
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0000965
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000654
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.000414
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000485
Gnomad OTH
AF:
0.00143
GnomAD3 exomes
AF:
0.000588
AC:
143
AN:
243236
Hom.:
0
AF XY:
0.000651
AC XY:
86
AN XY:
132076
show subpopulations
Gnomad AFR exome
AF:
0.0000635
Gnomad AMR exome
AF:
0.00183
Gnomad ASJ exome
AF:
0.00139
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000302
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.000428
Gnomad OTH exome
AF:
0.00205
GnomAD4 exome
AF:
0.000333
AC:
484
AN:
1454758
Hom.:
0
AF XY:
0.000352
AC XY:
255
AN XY:
723632
show subpopulations
Gnomad4 AFR exome
AF:
0.0000905
Gnomad4 AMR exome
AF:
0.00181
Gnomad4 ASJ exome
AF:
0.00110
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000363
Gnomad4 FIN exome
AF:
0.0000191
Gnomad4 NFE exome
AF:
0.000262
Gnomad4 OTH exome
AF:
0.000650
GnomAD4 genome
AF:
0.000342
AC:
52
AN:
152246
Hom.:
0
Cov.:
33
AF XY:
0.000228
AC XY:
17
AN XY:
74436
show subpopulations
Gnomad4 AFR
AF:
0.0000963
Gnomad4 AMR
AF:
0.000654
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.000414
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000485
Gnomad4 OTH
AF:
0.00142
Alfa
AF:
0.000695
Hom.:
0
Bravo
AF:
0.000412

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

CD93-related disorder Benign:1
Likely benign, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesNov 27, 2023This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs556056799; hg19: chr20-23065375; API