chr17-74706775-C-T

Variant names:

• chr17-74706775-C-T
• rs1037170
• NM_139018.5:c.44-1959G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CD300LF	NM_139018.5	c.44-1959G>A		intron_variant	Intron 1 of 6	ENST00000326165.11	NP_620587.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD300LF	ENST00000326165.11	c.44-1959G>A		intron_variant	Intron 1 of 6	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

African (AFR) AF: 0.163 AC: 6773 AN: 41492

American (AMR) AF: 0.503 AC: 7685 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.808 AC: 2807 AN: 3472

East Asian (EAS) AF: 0.534 AC: 2759 AN: 5166

South Asian (SAS) AF: 0.632 AC: 3051 AN: 4830

European-Finnish (FIN) AF: 0.630 AC: 6655 AN: 10562

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.733 AC: 49824 AN: 68000

Other (OTH) AF: 0.589 AC: 1245 AN: 2112

Alfa AF: 0.667 Hom.: 110909

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
PhyloP100		-0.54
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: rs1037170; hg19: chr17-72702914;