rs905709

Variant names:

• chr17-74567282-T-C
• rs905709
• NM_001324073.3:c.61+1A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.851
• Publications: 5 publications found

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]

ACMG classification

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300H	NM_001324073.3	MANE Select	c.61+1A>G		splice_donor intron	N/A	NP_001311002.1	A0A0K2S4Q6-1
	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	A0A0K2S4Q6-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD300H	ENST00000641710.1		c.61+1A>G		splice_donor intron	N/A	ENSP00000492977.1	A0A0K2S4Q6-1
	CD300H	ENST00000641031.1		c.61+1A>G		splice_donor intron	N/A	ENSP00000492997.1	A0A0K2S4Q6-2

Frequencies

GnomAD3 genomes AF: 0.616 AC: 93658 AN: 151940 Hom.: 29802 Cov.: 32

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.: 47 AF XY: 0.558 AC XY: 284152 AN XY: 509600

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

GnomAD4 genome AF: 0.616 AC: 93720 AN: 152058 Hom.: 29820 Cov.: 32 AF XY: 0.614 AC XY: 45600 AN XY: 74314

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

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	18
DANN	Benign	0.74
PhyloP100		0.85

Splicing

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

Other links and lift over

dbSNP: rs905709; hg19: chr17-72563421;