Genetic Variant CD300LF:c.44-1959G>A (chr17-74706775-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.535

Publications

17 publications found

Variant links:

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]

CD300LF links:

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 links:

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new If you want to explore the variant's impact on the transcript NM_139018.5, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_139018.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD300LF	NM_139018.5	MANE Select	c.44-1959G>A	intron	N/A	NP_620587.2
CD300LF	NM_001289084.2		c.44-1959G>A	intron	N/A	NP_001276013.1	J3KS52
CD300LF	NM_001289085.2		c.-122-1398G>A	intron	N/A	NP_001276014.1	Q8TDQ1-6

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CD300LF	ENST00000326165.11	TSL:1 MANE Select	c.44-1959G>A	intron	N/A	ENSP00000327075.6	Q8TDQ1-1
CD300LF	ENST00000469092.5	TSL:1	c.-122-1398G>A	intron	N/A	ENSP00000463743.1	Q8TDQ1-4
CD300LF	ENST00000963433.1		c.44-1959G>A	intron	N/A	ENSP00000633492.1

Frequencies

GnomAD3 genomes

AF:

0.538

AC:

81785

AN:

151986

Hom.:

26614

Cov.:

show subpopulations

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.:

AF XY:

0.535

AC XY:

39807

AN XY:

74342

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1523

3047

4570

6094

7617

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

678

1356

2034

2712

3390

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.1

(source)

DANN

Benign

0.81

PhyloP100

-0.54

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over