17-74525958-G-T

Variant names:

• chr17-74525958-G-T
• rs752893026
• NM_174892.4:c.160C>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_174892.4(CD300LB):​c.160C>A​(p.Arg54Ser) 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. 16/20 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. R54H) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD300LB NM_174892.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -6.51
• Publications: 0 publications found

Genes affected

CD300LB (HGNC:30811): (CD300 molecule like family member b) CD300LB is a nonclassical activating receptor of the immunoglobulin (Ig) superfamily expressed on myeloid cells (Martinez-Barriocanal and Sayos, 2006 [PubMed 16920917]).[supplied by OMIM, Mar 2008]

ENSG00000289070 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.03822884).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174892.4. 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
	CD300LB	NM_174892.4	MANE Select	c.160C>A	p.Arg54Ser	missense	Exon 2 of 4	NP_777552.3	A8K4G0

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300LB	ENST00000392621.6	TSL:1 MANE Select	c.160C>A	p.Arg54Ser	missense	Exon 2 of 4	ENSP00000376397.2	A8K4G0
	CD300LB	ENST00000718280.1		c.160C>A	p.Arg54Ser	missense	Exon 2 of 4	ENSP00000520719.1	A8K4G0
	CD300LB	ENST00000314401.3	TSL:2	c.160C>A	p.Arg54Ser	missense	Exon 2 of 3	ENSP00000317337.4	J9JID3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.32	T
BayesDel_noAF	Benign	-0.69
CADD	Benign	0.0010
DANN	Benign	0.31
DEOGEN2	Benign	0.080	T
Eigen	Benign	-2.1
Eigen_PC	Benign	-2.2
FATHMM_MKL	Benign	0.0019	N
LIST_S2	Benign	0.0093	T
M_CAP	Benign	0.0016	T
MetaRNN	Benign	0.038	T
MetaSVM	Benign	-0.94	T
MutationAssessor	Benign	-0.14	N
PhyloP100		-6.5
PrimateAI	Benign	0.24	T
PROVEAN	Benign	0.29	N
REVEL	Benign	0.041
Sift	Benign	0.76	T
Sift4G	Benign	0.75	T
Polyphen		0.0040	B
Vest4		0.17
MutPred		0.38		Loss of solvent accessibility (P = 0.0238)
MVP		0.20
MPC		0.29
ClinPred		0.086	T
GERP RS		-10
Varity_R		0.093
gMVP		0.28

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: rs752893026; hg19: chr17-72522097;