17-74706775-C-T

Position:

• chr17-74706775-C-T

Variant summary

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

The NM_139018.5(CD300LF):​c.44-1959G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.538 in 152,104 control chromosomes in the GnomAD database, including 26,616 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 0.54 (26616 hom., cov: 32)
• Consequence: CD300LF NM_139018.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.535

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]

RAB37 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CD300LF	NM_139018.5	c.44-1959G>A		intron_variant		ENST00000326165.11	NP_620587.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CD300LF	ENST00000326165.11	c.44-1959G>A		intron_variant		1	NM_139018.5	ENSP00000327075.6

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81785 AN: 151986 Hom.: 26614 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.821

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.808

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.733

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.538 AC: 81777 AN: 152104 Hom.: 26616 Cov.: 32 AF XY: 0.535 AC XY: 39807 AN XY: 74342

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.503

Gnomad4 ASJ AF: 0.808

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.632

Gnomad4 FIN AF: 0.630

Gnomad4 NFE AF: 0.733

Gnomad4 OTH AF: 0.589

Alfa AF: 0.707 Hom.: 77799

Bravo AF: 0.511

Asia WGS AF: 0.509 AC: 1770 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.81

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: rs1037170; hg19: chr17-72702914;