NM_014880.5:c.13G>A

Variant names:

• chr2-159798186-C-T
• rs374135673
• NM_014880.5:c.13G>A

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_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. 15/21 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
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.787
• Publications: 0 publications found

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]

LOC124906083 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0042333603).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014880.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD302	NM_014880.5	MANE Select	c.13G>A	p.Ala5Thr	missense	Exon 1 of 6	NP_055695.2
	CD302	NM_001198764.2		c.13G>A	p.Ala5Thr	missense	Exon 1 of 5	NP_001185693.1	A0A087WT00
	CD302	NM_001198763.2		c.13G>A	p.Ala5Thr	missense	Exon 1 of 5	NP_001185692.1	Q8IX05-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD302	ENST00000259053.6	TSL:1 MANE Select	c.13G>A	p.Ala5Thr	missense	Exon 1 of 6	ENSP00000259053.4	Q8IX05-1
	LY75-CD302	ENST00000504764.5	TSL:2	c.4990+8787G>A		intron	N/A	ENSP00000423463.1
	CD302	ENST00000966883.1		c.13G>A	p.Ala5Thr	missense	Exon 1 of 7	ENSP00000636942.1

Frequencies

GnomAD3 genomes AF: 0.0000735 AC: 11 AN: 149750 Hom.: 0 Cov.: 33

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

GnomAD2 exomes AF: 0.000176 AC: 14 AN: 79732 AF XY: 0.000219

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 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

African (AFR) AF: 0.00 AC: 0 AN: 25934

American (AMR) AF: 0.00 AC: 0 AN: 26326

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23204

East Asian (EAS) AF: 0.000566 AC: 16 AN: 28250

South Asian (SAS) AF: 0.0000687 AC: 5 AN: 72772

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 34262

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4466

European-Non Finnish (NFE) AF: 9.54e-7 AC: 1 AN: 1048534

Other (OTH) AF: 0.0000917 AC: 5 AN: 54532

GnomAD4 genome AF: 0.0000734 AC: 11 AN: 149842 Hom.: 0 Cov.: 33 AF XY: 0.0000682 AC XY: 5 AN XY: 73284

African (AFR) AF: 0.00 AC: 0 AN: 39364

American (AMR) AF: 0.00 AC: 0 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00193 AC: 10 AN: 5170

South Asian (SAS) AF: 0.00 AC: 0 AN: 4824

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10570

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 67940

Other (OTH) AF: 0.000481 AC: 1 AN: 2080

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

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

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
M_CAP	Benign	0.026	D
MetaRNN	Benign	0.0042	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.55	N
PhyloP100		0.79
PROVEAN	Benign	0.22	N
REVEL	Benign	0.012
Sift	Benign	0.17	T
Sift4G	Benign	0.23	T
Polyphen		0.0	B
Vest4		0.19
MutPred		0.33		Loss of helix (P = 0.0093)
MVP		0.14
MPC		0.047
ClinPred		0.012	T
GERP RS		0.90
PromoterAI		-0.15	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0
Varity_R		0.039
gMVP		0.31
Mutation Taster		=94/6	polymorphism

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

Other links and lift over

dbSNP: rs374135673; hg19: chr2-160654697;