rs4788837

Positions:

• chr17-74470080-G-A

Variant summary

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

The ENST00000577511(CD300A):​c.-513G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.456 in 984,610 control chromosomes in the GnomAD database, including 108,272 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 0.57 (27268 hom., cov: 31)
  • Exomes 𝑓: 0.43 (81004 hom.)
• Consequence: CD300A ENST00000577511 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.152

Genes affected

CD300A (HGNC:19319): (CD300a molecule) This gene encodes a member of the CD300 glycoprotein family of cell surface proteins found on leukocytes involved in immune response signaling pathways. This gene is located on chromosome 17 in a cluster with all but one of the other family members. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2012]

CD300A (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD300A	NM_007261.4	c.40+3337G>A		intron_variant		ENST00000360141.8	NP_009192.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD300A	ENST00000360141.8	c.40+3337G>A		intron_variant		1	NM_007261.4	ENSP00000353259.3

Frequencies

GnomAD3 genomes AF: 0.569 AC: 86383 AN: 151792 Hom.: 27201 Cov.: 31

Gnomad AFR AF: 0.839

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.556

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.554

GnomAD4 exome AF: 0.435 AC: 362056 AN: 832696 Hom.: 81004 Cov.: 31 AF XY: 0.434 AC XY: 167040 AN XY: 384558

Gnomad4 AFR exome AF: 0.875

Gnomad4 AMR exome AF: 0.616

Gnomad4 ASJ exome AF: 0.440

Gnomad4 EAS exome AF: 0.725

Gnomad4 SAS exome AF: 0.548

Gnomad4 FIN exome AF: 0.442

Gnomad4 NFE exome AF: 0.420

Gnomad4 OTH exome AF: 0.475

GnomAD4 genome AF: 0.570 AC: 86517 AN: 151914 Hom.: 27268 Cov.: 31 AF XY: 0.574 AC XY: 42637 AN XY: 74226

Gnomad4 AFR AF: 0.839

Gnomad4 AMR AF: 0.617

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.559

Alfa AF: 0.466 Hom.: 10803

Bravo AF: 0.594

Asia WGS AF: 0.687 AC: 2389 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.59

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: rs4788837; hg19: chr17-72466219;