rs3789205

Positions:

• chr6-41286177-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018643.5(TREM1):​c.49+430T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0971 in 152,230 control chromosomes in the GnomAD database, including 890 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 0.097 (890 hom., cov: 32)
• Consequence: TREM1 NM_018643.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.607

Genes affected

TREM1 (HGNC:17760): (triggering receptor expressed on myeloid cells 1) This gene encodes a receptor belonging to the Ig superfamily that is expressed on myeloid cells. This protein amplifies neutrophil and monocyte-mediated inflammatory responses triggered by bacterial and fungal infections by stimulating release of pro-inflammatory chemokines and cytokines, as well as increased surface expression of cell activation markers. Alternatively spliced transcript variants encoding different isoforms have been noted for this gene.[provided by RefSeq, Jun 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TREM1	NM_018643.5	c.49+430T>C		intron_variant		ENST00000244709.9	NP_061113.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TREM1	ENST00000244709.9	c.49+430T>C		intron_variant		1	NM_018643.5	ENSP00000244709	P2

Frequencies

GnomAD3 genomes AF: 0.0971 AC: 14770 AN: 152112 Hom.: 884 Cov.: 32

Gnomad AFR AF: 0.0587

Gnomad AMI AF: 0.0890

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.0773

Gnomad EAS AF: 0.307

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.0982

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0971 AC: 14784 AN: 152230 Hom.: 890 Cov.: 32 AF XY: 0.101 AC XY: 7481 AN XY: 74420

Gnomad4 AFR AF: 0.0586

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.0773

Gnomad4 EAS AF: 0.307

Gnomad4 SAS AF: 0.130

Gnomad4 FIN AF: 0.122

Gnomad4 NFE AF: 0.0939

Gnomad4 OTH AF: 0.105

Alfa AF: 0.103 Hom.: 93

Bravo AF: 0.0977

Asia WGS AF: 0.210 AC: 729 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.9
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3789205; hg19: chr6-41253915;