chr2-159798186-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_014880.5(CD302):​c.13G>A​(p.Ala5Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000259 in 1,468,122 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000073 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000020 ( 0 hom. )

Consequence

CD302
NM_014880.5 missense

Scores

18

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 0.787
Variant links:
Genes affected
CD302 (HGNC:30843): (CD302 molecule) CD302 is a C-type lectin receptor involved in cell adhesion and migration, as well as endocytosis and phagocytosis (Kato et al., 2007 [PubMed 17947679]).[supplied by OMIM, Aug 2008]
LY75-CD302 (HGNC:38828): (LY75-CD302 readthrough) This locus represents naturally occurring read-through transcription between the neighboring lymphocyte antigen 75 (LY75) and CD302 molecule (CD302) genes. Alternative splicing results in multiple transcript variants encoding fusion products that share sequence identity with each individual gene product. [provided by RefSeq, Nov 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.0042333603).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CD302NM_014880.5 linkuse as main transcriptc.13G>A p.Ala5Thr missense_variant 1/6 ENST00000259053.6 NP_055695.2 Q8IX05-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CD302ENST00000259053.6 linkuse as main transcriptc.13G>A p.Ala5Thr missense_variant 1/61 NM_014880.5 ENSP00000259053.4 Q8IX05-1
LY75-CD302ENST00000504764.5 linkuse as main transcriptc.4990+8787G>A intron_variant 2 ENSP00000423463.1

Frequencies

GnomAD3 genomes
AF:
0.0000735
AC:
11
AN:
149750
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00193
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000486
GnomAD3 exomes
AF:
0.000176
AC:
14
AN:
79732
Hom.:
0
AF XY:
0.000219
AC XY:
10
AN XY:
45706
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00325
Gnomad SAS exome
AF:
0.000179
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.000434
GnomAD4 exome
AF:
0.0000205
AC:
27
AN:
1318280
Hom.:
0
Cov.:
32
AF XY:
0.0000185
AC XY:
12
AN XY:
650222
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000566
Gnomad4 SAS exome
AF:
0.0000687
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
9.54e-7
Gnomad4 OTH exome
AF:
0.0000917
GnomAD4 genome
AF:
0.0000734
AC:
11
AN:
149842
Hom.:
0
Cov.:
33
AF XY:
0.0000682
AC XY:
5
AN XY:
73284
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000481
Alfa
AF:
0.0000712
Hom.:
0
Bravo
AF:
0.0000378
ExAC
AF:
0.000206
AC:
5
Asia WGS
AF:
0.00289
AC:
10
AN:
3470

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsFeb 28, 2023The c.13G>A (p.A5T) alteration is located in exon 1 (coding exon 1) of the CD302 gene. This alteration results from a G to A substitution at nucleotide position 13, causing the alanine (A) at amino acid position 5 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.30
BayesDel_addAF
Benign
-0.60
T
BayesDel_noAF
Benign
-0.64
CADD
Benign
7.5
DANN
Benign
0.87
DEOGEN2
Benign
0.098
.;.;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Benign
0.053
N
LIST_S2
Benign
0.35
T;T;T
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.0042
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.55
N;.;N
PROVEAN
Benign
0.22
N;.;N
REVEL
Benign
0.012
Sift
Benign
0.17
T;.;T
Sift4G
Benign
0.23
T;T;T
Polyphen
0.0
.;.;B
Vest4
0.19
MutPred
0.33
Loss of helix (P = 0.0093);Loss of helix (P = 0.0093);Loss of helix (P = 0.0093);
MVP
0.14
MPC
0.047
ClinPred
0.012
T
GERP RS
0.90
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.039
gMVP
0.31

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: rs374135673; hg19: chr2-160654697; API