17-74588605-C-T

Variant names:

• chr17-74588605-C-T
• NM_001115152.2:c.285G>A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2 BP4_Strong BP6_Moderate BP7

The NM_001115152.2(CD300LD):​c.285G>A​(p.Glu95Glu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CD300LD NM_001115152.2 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.0630

Genes affected

CD300LD (HGNC:16848): (CD300 molecule like family member d) Predicted to enable transmembrane signaling receptor activity and virus receptor activity. Predicted to be involved in immune system process. Predicted to act upstream of or within regulation of interleukin-6 production and regulation of tumor necrosis factor production. Predicted to be integral component of membrane. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

CD300LD-AS1 (HGNC:26480): (CD300LD antisense RNA 1) Predicted to be located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BP6: Variant 17-74588605-C-T is Benign according to our data. Variant chr17-74588605-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2648225.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=0.063 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CD300LD	NM_001115152.2	c.285G>A	p.Glu95Glu	synonymous_variant	Exon 2 of 4	ENST00000375352.1	NP_001108624.1
CD300LD	XM_047435046.1	c.264G>A	p.Glu88Glu	synonymous_variant	Exon 1 of 3		XP_047291002.1
CD300LD-AS1	NR_171003.1	n.237-1914C>T		intron_variant	Intron 1 of 2
CD300LD-AS1	NR_171004.1	n.73-1914C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CD300LD	ENST00000375352.1	c.285G>A	p.Glu95Glu	synonymous_variant	Exon 2 of 4	1	NM_001115152.2	ENSP00000364501.1
CD300LD-AS1	ENST00000392620.5	n.73-1914C>T		intron_variant	Intron 1 of 2	2
CD300LD-AS1	ENST00000524389.5	n.237-1914C>T		intron_variant	Intron 1 of 2	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Sep 01, 2022

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CD300LD: PM2:Supporting, BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	4.7
DANN	Benign	0.77

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr17-72584744;