17-74703694-T-C

Variant summary

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

The NM_139018.5(CD300LF):c.383-596A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.661 in 152,070 control chromosomes in the GnomAD database, including 36,287 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 0.66 (36287 hom., cov: 32)
• Consequence: CD300LF NM_139018.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

Genes affected

CD300LF (HGNC:29883): (CD300 molecule like family member f) This gene encodes a member of the CD300 protein family. Members of this family are cell surface glycoproteins with a single IgV-like extracellular domain, and are involved in the regulation of immune response. The encoded protein is an inhibitory receptor. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

RAB37 (HGNC:30268): (RAB37, member RAS oncogene family) Rab proteins are low molecular mass GTPases that are critical regulators of vesicle trafficking. For additional background information on Rab proteins, see MIM 179508.[supplied by OMIM, Apr 2006]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD300LF	NM_139018.5	c.383-596A>G		intron_variant		ENST00000326165.11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD300LF	ENST00000326165.11	c.383-596A>G		intron_variant		1	NM_139018.5

Frequencies

GnomAD3 genomes AF: 0.661 AC: 100467 AN: 151950 Hom.: 36283 Cov.: 32

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.937

Gnomad AMR AF: 0.605

Gnomad ASJ AF: 0.838

Gnomad EAS AF: 0.727

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.689

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

GnomAD4 genome AF: 0.661 AC: 100506 AN: 152070 Hom.: 36287 Cov.: 32 AF XY: 0.661 AC XY: 49108 AN XY: 74346

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.838

Gnomad4 EAS AF: 0.727

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.687

Alfa AF: 0.799 Hom.: 107709

Bravo AF: 0.635

Asia WGS AF: 0.673 AC: 2344 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.8
Dann	Benign	0.77

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: rs10512597; hg19: chr17-72699833;