rs10512596

chr17-74527085-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174892.4(CD300LB):c.41-1008A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,162 control chromosomes in the GnomAD database, including 21,959 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (21959 hom., cov: 33)
• Consequence: CD300LB NM_174892.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117

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]

LOC107985074 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD300LB	NM_174892.4	c.41-1008A>G		intron_variant		ENST00000392621.6
LOC107985074	XR_007065902.1	n.353-5462T>C		intron_variant, non_coding_transcript_variant
CD300LB	XM_005257027.4	c.152-1008A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD300LB	ENST00000392621.6	c.41-1008A>G		intron_variant		1	NM_174892.4	P2
CD300LB	ENST00000314401.3	c.41-1008A>G		intron_variant		2		A2

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80622 AN: 152044 Hom.: 21957 Cov.: 33

Gnomad AFR AF: 0.510

Gnomad AMI AF: 0.656

Gnomad AMR AF: 0.481

Gnomad ASJ AF: 0.609

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.690

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.562

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.530 AC: 80660 AN: 152162 Hom.: 21959 Cov.: 33 AF XY: 0.524 AC XY: 38973 AN XY: 74396

Gnomad4 AFR AF: 0.511

Gnomad4 AMR AF: 0.481

Gnomad4 ASJ AF: 0.609

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.555

Alfa AF: 0.569 Hom.: 33866

Bravo AF: 0.528

Asia WGS AF: 0.343 AC: 1195 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	4.2
Dann	Benign	0.41

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

Other links and lift over

dbSNP: rs10512596; hg19: chr17-72523224;