17-43853846-A-C

Position:

• chr17-43853846-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The ENST00000317310.5(CD300LG):​c.521A>C​(p.Gln174Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD300LG ENST00000317310.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.499

Genes affected

CD300LG (HGNC:30455): (CD300 molecule like family member g) Members of the CD300 (see MIM 606786)-like (CD300L) family, such as CD300LG, are widely expressed on hematopoietic cells. All CD300L proteins are type I cell surface glycoproteins that contain a single immunoglobulin (Ig) V-like domain (Takatsu et al., 2006 [PubMed 16876123]).[supplied by OMIM, Mar 2008]

LOC107985077 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.19836977).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD300LG	NM_145273.4	c.521A>C	p.Gln174Pro	missense_variant	4/7	ENST00000317310.5	NP_660316.2
LOC107985077	XR_001752896.2	n.180+565T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD300LG	ENST00000317310.5	c.521A>C	p.Gln174Pro	missense_variant	4/7	1	NM_145273.4	ENSP00000321005	P2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 06, 2023

The c.521A>C (p.Q174P) alteration is located in exon 4 (coding exon 4) of the CD300LG gene. This alteration results from a A to C substitution at nucleotide position 521, causing the glutamine (Q) at amino acid position 174 to be replaced by a proline (P). 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	0.064
BayesDel_addAF	Benign	-0.15	T
BayesDel_noAF	Benign	-0.46
CADD	Benign	21
DANN	Uncertain	0.99
DEOGEN2	Benign	0.036	.;.;T
Eigen	Benign	0.086
Eigen_PC	Benign	0.032
FATHMM_MKL	Benign	0.61	D
LIST_S2	Benign	0.53	T;T;T
M_CAP	Benign	0.012	T
MetaRNN	Benign	0.20	T;T;T
MetaSVM	Benign	-1.1	T
MutationAssessor	Benign	1.6	.;L;L
MutationTaster	Benign	1.0	D;D;N;N;N
PrimateAI	Benign	0.30	T
PROVEAN	Benign	-1.8	N;N;N
REVEL	Benign	0.069
Sift	Benign	0.44	T;T;T
Sift4G	Benign	0.26	T;T;T
Polyphen		1.0	.;.;D
Vest4		0.35
MutPred		0.21		.;Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP		0.42
MPC		0.29
ClinPred		0.85	D
GERP RS		1.5
Varity_R		0.25
gMVP		0.53

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: chr17-41931214;