NM_181449.3:c.40+496C>T

Variant names:

• chr17-74623086-G-A
• rs1699607
• NM_181449.3:c.40+496C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_181449.3(CD300E):​c.40+496C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.494 in 152,012 control chromosomes in the GnomAD database, including 18,757 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 0.49 (18757 hom., cov: 32)
• Consequence: CD300E NM_181449.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0320
• Publications: 10 publications found

Genes affected

CD300E (HGNC:28874): (CD300e molecule) This gene encodes a member of the CD300 glycoprotein family of cell surface proteins expressed on myeloid cells. The protein interacts with the TYRO protein tyrosine kinase-binding protein and is thought to act as an activating receptor. [provided by RefSeq, Nov 2012]

CD300LD-AS1 (HGNC:26480): (CD300LD antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

LOC101928343 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD300E	NM_181449.3	c.40+496C>T		intron_variant	Intron 1 of 3	ENST00000392619.2	NP_852114.2
LOC101928343	NR_158152.1	n.2504-2441G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD300E	ENST00000392619.2	c.40+496C>T		intron_variant	Intron 1 of 3	1	NM_181449.3	ENSP00000376395.2
CD300LD-AS1	ENST00000838315.1	n.572-2441G>A		intron_variant	Intron 3 of 3
CD300LD-AS1	ENST00000838318.1	n.605-2441G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.494 AC: 75067 AN: 151894 Hom.: 18745 Cov.: 32

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.426

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.494 AC: 75116 AN: 152012 Hom.: 18757 Cov.: 32 AF XY: 0.488 AC XY: 36263 AN XY: 74336

African (AFR) AF: 0.535 AC: 22183 AN: 41466

American (AMR) AF: 0.426 AC: 6500 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.428 AC: 1484 AN: 3468

East Asian (EAS) AF: 0.423 AC: 2184 AN: 5162

South Asian (SAS) AF: 0.396 AC: 1904 AN: 4814

European-Finnish (FIN) AF: 0.464 AC: 4898 AN: 10564

Middle Eastern (MID) AF: 0.408 AC: 120 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34283 AN: 67958

Other (OTH) AF: 0.487 AC: 1027 AN: 2110

Alfa AF: 0.492 Hom.: 24813

Bravo AF: 0.495

Asia WGS AF: 0.385 AC: 1340 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.9
DANN	Benign	0.89
PhyloP100		0.032
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: rs1699607; hg19: chr17-72619225;