Genetic Variant CD300LB:p.Leu170Leu (chr17-74522834-G-T) – ACMG Classification: Benign (-11 pts)

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_174892.4(CD300LB):c.510C>A(p.Leu170Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00282 in 1,614,122 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.0025 ( 2 hom., cov: 32)

Exomes 𝑓: 0.0029 ( 8 hom. )

Consequence

CD300LB
NM_174892.4 synonymous

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 2.28

Variant links:

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]

CD300LB links:

LOC107985074 (HGNC:):

LOC107985074 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.54).

BP6

Variant 17-74522834-G-T is Benign according to our data. Variant chr17-74522834-G-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648224.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=2.28 with no splicing effect.

BS2

High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD300LB	NM_174892.4 link	c.510C>A	p.Leu170Leu	synonymous_variant	Exon 4 of 4	ENST00000392621.6	NP_777552.3	A8K4G0
CD300LB	XM_005257027.4 link	c.554+745C>A		intron_variant	Intron 3 of 3		XP_005257084.1
LOC107985074	XR_007065902.1 link	n.352+1452G>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD300LB	ENST00000392621.6 link	c.510C>A	p.Leu170Leu	synonymous_variant	Exon 4 of 4	1	NM_174892.4	ENSP00000376397.2		A8K4G0

Frequencies

GnomAD3 genomes

AF:

0.00246

AC:

375

AN:

152138

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000459

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.000589

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00556

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00350

Gnomad OTH

AF:

0.00239

GnomAD3 exomes

AF:

0.00241

AC:

605

AN:

251450

Hom.:

AF XY:

0.00235

AC XY:

320

AN XY:

135892

show subpopulations

Gnomad AFR exome

AF:

0.000677

Gnomad AMR exome

AF:

0.000752

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00105

Gnomad FIN exome

AF:

0.00397

Gnomad NFE exome

AF:

0.00382

Gnomad OTH exome

AF:

0.00244

GnomAD4 exome

AF:

0.00285

AC:

4173

AN:

1461866

Hom.:

Cov.:

AF XY:

0.00275

AC XY:

1997

AN XY:

727230

show subpopulations

Gnomad4 AFR exome

AF:

0.00105

Gnomad4 AMR exome

AF:

0.000783

Gnomad4 ASJ exome

AF:

0.000115

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000939

Gnomad4 FIN exome

AF:

0.00429

Gnomad4 NFE exome

AF:

0.00328

Gnomad4 OTH exome

AF:

0.00225

GnomAD4 genome

AF:

0.00246

AC:

375

AN:

152256

Hom.:

Cov.:

AF XY:

0.00266

AC XY:

198

AN XY:

74442

show subpopulations

Gnomad4 AFR

AF:

0.000457

Gnomad4 AMR

AF:

0.000588

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00556

Gnomad4 NFE

AF:

0.00350

Gnomad4 OTH

AF:

0.00237

Alfa

AF:

0.00221

Hom.:

Bravo

AF:

0.00202

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00251

EpiControl

AF:

0.00320

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Aug 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CD300LB: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.54

CADD

Benign

4.8

DANN

Benign

0.65

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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over