dbSNP rs4788837: CD300A:c.-513G>A (chr17-74470080-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000577511.1(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
ENST00000577511.1 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.152

Publications

9 publications found

Variant links:

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 links:

Genome browser will be placed here

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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.831 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000577511.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD300A	NM_007261.4	MANE Select	c.40+3337G>A	intron	N/A	NP_009192.2
CD300A	NM_001256841.2		c.40+3337G>A	intron	N/A	NP_001243770.1
CD300A	NM_001330456.1		c.-351+3425G>A	intron	N/A	NP_001317385.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD300A	ENST00000577511.1	TSL:1	c.-513G>A	5_prime_UTR	Exon 2 of 8	ENSP00000463189.1
CD300A	ENST00000360141.8	TSL:1 MANE Select	c.40+3337G>A	intron	N/A	ENSP00000353259.3
CD300A	ENST00000310828.10	TSL:1	c.40+3337G>A	intron	N/A	ENSP00000308188.5

Frequencies

GnomAD3 genomes

AF:

0.569

AC:

86383

AN:

151792

Hom.:

27201

Cov.:

show subpopulations

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.:

AF XY:

0.434

AC XY:

167040

AN XY:

384558

show subpopulations

African (AFR)

AF:

0.875

AC:

13803

AN:

15782

American (AMR)

AF:

0.616

AC:

606

AN:

984

Ashkenazi Jewish (ASJ)

AF:

0.440

AC:

2267

AN:

5154

East Asian (EAS)

AF:

0.725

AC:

2631

AN:

3630

South Asian (SAS)

AF:

0.548

AC:

9019

AN:

16448

European-Finnish (FIN)

AF:

0.442

AC:

123

AN:

278

Middle Eastern (MID)

AF:

0.459

AC:

743

AN:

1620

European-Non Finnish (NFE)

AF:

0.420

AC:

319914

AN:

761516

Other (OTH)

AF:

0.475

AC:

12950

AN:

27284

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.460

Heterozygous variant carriers

10098

20196

30295

40393

50491

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13594

27188

40782

54376

67970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.570

AC:

86517

AN:

151914

Hom.:

27268

Cov.:

AF XY:

0.574

AC XY:

42637

AN XY:

74226

show subpopulations

African (AFR)

AF:

0.839

AC:

34774

AN:

41464

American (AMR)

AF:

0.617

AC:

9399

AN:

15240

Ashkenazi Jewish (ASJ)

AF:

0.439

AC:

1521

AN:

3468

East Asian (EAS)

AF:

0.713

AC:

3687

AN:

5172

South Asian (SAS)

AF:

0.558

AC:

2684

AN:

4812

European-Finnish (FIN)

AF:

0.422

AC:

4435

AN:

10516

Middle Eastern (MID)

AF:

0.445

AC:

130

AN:

292

European-Non Finnish (NFE)

AF:

0.418

AC:

28430

AN:

67934

Other (OTH)

AF:

0.559

AC:

1177

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1623

3245

4868

6490

8113

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

710

1420

2130

2840

3550

<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:

0.478

Hom.:

18153

Bravo

AF:

0.594

Asia WGS

AF:

0.687

AC:

2389

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.59

PhyloP100

-0.15

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over