rs199745035

Variant summary

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

The NM_181449.3(CD300E):​c.478G>T​(p.Val160Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,340 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V160M) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

CD300E
NM_181449.3 missense

Scores

17

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.82
Variant links:
Genes affected
CD300E (HGNC:28874): (CD300e molecule) This gene encodes a member of the CD300 glycoprotein family of cell surface proteins expressed on myeloid cells. The protein interacts with the TYRO protein tyrosine kinase-binding protein and is thought to act as an activating receptor. [provided by RefSeq, Nov 2012]

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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=0.04845199).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CD300ENM_181449.3 linkc.478G>T p.Val160Leu missense_variant Exon 3 of 4 ENST00000392619.2 NP_852114.2 Q496F6B4E0V9
LOC101928343NR_158152.1 linkn.2503+7318C>A intron_variant Intron 3 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CD300EENST00000392619.2 linkc.478G>T p.Val160Leu missense_variant Exon 3 of 4 1 NM_181449.3 ENSP00000376395.2 Q496F6

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461340
Hom.:
0
Cov.:
29
AF XY:
0.00000138
AC XY:
1
AN XY:
726918
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
8.99e-7
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.72
CADD
Benign
0.16
DANN
Benign
0.56
DEOGEN2
Benign
0.029
T
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.5
FATHMM_MKL
Benign
0.0066
N
LIST_S2
Benign
0.46
T
M_CAP
Benign
0.0044
T
MetaRNN
Benign
0.048
T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.1
L
PrimateAI
Benign
0.28
T
REVEL
Benign
0.0040
Sift4G
Benign
0.33
T
Polyphen
0.14
B
Vest4
0.033
MutPred
0.28
Loss of sheet (P = 0.0315);
MVP
0.12
ClinPred
0.10
T
GERP RS
-3.6
Varity_R
0.041
gMVP
0.27

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-72610083; API