Genetic Variant CD300H:c.61+1A>G (chr17-74567282-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001324073.3(CD300H):c.61+1A>G variant causes a splice donor, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 1,231,584 control chromosomes in the GnomAD database, including 198,555 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 0.62 ( 29820 hom., cov: 32)

Exomes 𝑓: 0.56 ( 168735 hom. )

Consequence

CD300H
NM_001324073.3 splice_donor, intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.851

Publications

5 publications found

Variant links:

Genes affected

CD300H (HGNC:52292): (CD300H molecule (gene/pseudogene)) This gene belongs to the CD300 gene family, which in turn, belongs to the immunoglobulin (Ig) superfamily. This gene is located within a CD300 cluster on chromosome 17. The encoded protein may be involved in innate immunity as well as autoimmune response. A G>A mutation, represented by the single nucleotide polymorphism (SNP) rs905709, at the splice donor site of the 5' terminal exon may be associated with lack of expression of this gene in homozygous (AA) individuals. The human reference assembly (GRCh38.p2) represents the 'A' allele at this SNP. [provided by RefSeq, Apr 2016]

CD300H links:

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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=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001324073.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
CD300H	NM_001324073.3	MANE Select	c.61+1A>G	splice_donor intron	N/A	NP_001311002.1
CD300H	NM_001405511.1		c.-33+67A>G	intron	N/A	NP_001392440.1
CD300H	NM_001324076.3		c.61+1A>G	splice_donor intron	N/A	NP_001311005.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300H	ENST00000641710.1		c.61+1A>G		splice_donor intron	N/A	ENSP00000492977.1
	CD300H	ENST00000641031.1		c.61+1A>G		splice_donor intron	N/A	ENSP00000492997.1

Frequencies

GnomAD3 genomes

AF:

0.616

AC:

93658

AN:

151940

Hom.:

29802

Cov.:

show subpopulations

Gnomad AFR

AF:

0.776

Gnomad AMI

AF:

0.557

Gnomad AMR

AF:

0.497

Gnomad ASJ

AF:

0.604

Gnomad EAS

AF:

0.535

Gnomad SAS

AF:

0.571

Gnomad FIN

AF:

0.614

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.557

Gnomad OTH

AF:

0.636

GnomAD4 exome

AF:

0.558

AC:

602337

AN:

1079526

Hom.:

168735

Cov.:

AF XY:

0.558

AC XY:

284152

AN XY:

509600

show subpopulations

African (AFR)

AF:

0.794

AC:

18224

AN:

22966

American (AMR)

AF:

0.470

AC:

3957

AN:

8416

Ashkenazi Jewish (ASJ)

AF:

0.608

AC:

8754

AN:

14394

East Asian (EAS)

AF:

0.525

AC:

13924

AN:

26524

South Asian (SAS)

AF:

0.559

AC:

10888

AN:

19492

European-Finnish (FIN)

AF:

0.608

AC:

12876

AN:

21168

Middle Eastern (MID)

AF:

0.601

AC:

1753

AN:

2916

European-Non Finnish (NFE)

AF:

0.551

AC:

506949

AN:

919968

Other (OTH)

AF:

0.573

AC:

25012

AN:

43682

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.475

Heterozygous variant carriers

14796

29592

44389

59185

73981

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

16534

33068

49602

66136

82670

<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:

0.616

AC:

93720

AN:

152058

Hom.:

29820

Cov.:

AF XY:

0.614

AC XY:

45600

AN XY:

74314

show subpopulations

African (AFR)

AF:

0.776

AC:

32211

AN:

41500

American (AMR)

AF:

0.496

AC:

7579

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.604

AC:

2094

AN:

3468

East Asian (EAS)

AF:

0.536

AC:

2768

AN:

5166

South Asian (SAS)

AF:

0.569

AC:

2738

AN:

4812

European-Finnish (FIN)

AF:

0.614

AC:

6482

AN:

10558

Middle Eastern (MID)

AF:

0.582

AC:

171

AN:

294

European-Non Finnish (NFE)

AF:

0.557

AC:

37830

AN:

67968

Other (OTH)

AF:

0.635

AC:

1339

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1808

3616

5425

7233

9041

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.580

Hom.:

8922

Bravo

AF:

0.616

Asia WGS

AF:

0.560

AC:

1947

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.74

PhyloP100

0.85

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over