rs17328707

chr6-41191415-G-A

Variant summary

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

The NM_024807.4(TREML2):c.*1012C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0933 in 152,322 control chromosomes in the GnomAD database, including 742 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 0.093 (741 hom., cov: 31)
  • Exomes 𝑓: 0.12 (1 hom.)
• Consequence: TREML2 NM_024807.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0920

Genes affected

TREML2 (HGNC:21092): (triggering receptor expressed on myeloid cells like 2) TREML2 is located in a gene cluster on chromosome 6 with the single Ig variable (IgV) domain activating receptors TREM1 (MIM 605085) and TREM2 (MIM 605086), but it has distinct structural and functional properties (Allcock et al., 2003 [PubMed 12645956]).[supplied by OMIM, Mar 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.123 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TREML2	NM_024807.4	c.*1012C>T		3_prime_UTR_variant	5/5	ENST00000483722.2
TREML2	XM_011514917.3	c.*1012C>T		3_prime_UTR_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TREML2	ENST00000483722.2	c.*1012C>T		3_prime_UTR_variant	5/5	1	NM_024807.4	P1

Frequencies

GnomAD3 genomes AF: 0.0933 AC: 14184 AN: 151984 Hom.: 741 Cov.: 31

Gnomad AFR AF: 0.0476

Gnomad AMI AF: 0.0976

Gnomad AMR AF: 0.0792

Gnomad ASJ AF: 0.124

Gnomad EAS AF: 0.0530

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0845

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.0970

GnomAD4 exome AF: 0.118 AC: 26 AN: 220 Hom.: 1 Cov.: 0 AF XY: 0.133 AC XY: 22 AN XY: 166

Gnomad4 AFR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.250

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.140

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.0933 AC: 14188 AN: 152102 Hom.: 741 Cov.: 31 AF XY: 0.0905 AC XY: 6729 AN XY: 74334

Gnomad4 AFR AF: 0.0476

Gnomad4 AMR AF: 0.0791

Gnomad4 ASJ AF: 0.124

Gnomad4 EAS AF: 0.0531

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0845

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.0970

Alfa AF: 0.117 Hom.: 1055

Bravo AF: 0.0904

Asia WGS AF: 0.114 AC: 396 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.1
Dann	Benign	0.26

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

LitVar

Other links and lift over

dbSNP: rs17328707; hg19: chr6-41159153;