NM_174892.4:c.41-1008A>G

Variant names:

• chr17-74527085-T-C
• rs10512596
• NM_174892.4:c.41-1008A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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: Benign. The variant received -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 rank	MANE	Protein	UniProt
CD300LB	NM_174892.4	c.41-1008A>G		intron_variant	Intron 1 of 3	ENST00000392621.6	NP_777552.3
CD300LB	XM_005257027.4	c.152-1008A>G		intron_variant	Intron 1 of 3		XP_005257084.1
LOC107985074	XR_007065902.1	n.353-5462T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD300LB	ENST00000392621.6	c.41-1008A>G		intron_variant	Intron 1 of 3	1	NM_174892.4	ENSP00000376397.2
CD300LB	ENST00000718280.1	c.41-1008A>G		intron_variant	Intron 1 of 3			ENSP00000520719.1
CD300LB	ENST00000314401.3	c.41-1008A>G		intron_variant	Intron 1 of 2	2		ENSP00000317337.4
ENSG00000289070	ENST00000809917.1	n.347-5462T>C		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.511 AC: 21205 AN: 41530

American (AMR) AF: 0.481 AC: 7348 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.609 AC: 2114 AN: 3472

East Asian (EAS) AF: 0.240 AC: 1242 AN: 5180

South Asian (SAS) AF: 0.522 AC: 2518 AN: 4826

European-Finnish (FIN) AF: 0.512 AC: 5414 AN: 10584

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.572 AC: 38848 AN: 67960

Other (OTH) AF: 0.555 AC: 1173 AN: 2114

Alfa AF: 0.567 Hom.: 42190

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
PhyloP100		0.12
Mutation Taster		=100/0	polymorphism (auto)

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: rs10512596; hg19: chr17-72523224;