NM_024807.4:c.*1012C>T

Variant names:

• chr6-41191415-G-A
• rs17328707
• NM_024807.4:c.*1012C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TREML2	NM_024807.4	c.*1012C>T		3_prime_UTR_variant	Exon 5 of 5	ENST00000483722.2	NP_079083.2
TREML2	XM_011514917.3	c.*1012C>T		3_prime_UTR_variant	Exon 4 of 4		XP_011513219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TREML2	ENST00000483722.2	c.*1012C>T		3_prime_UTR_variant	Exon 5 of 5	1	NM_024807.4	ENSP00000418767.1

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

African (AFR) AF: 0.00 AC: 0 AN: 10

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 4

East Asian (EAS) AF: 0.00 AC: 0 AN: 4

South Asian (SAS) AF: 0.250 AC: 1 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.140 AC: 25 AN: 178

Other (OTH) AF: 0.00 AC: 0 AN: 10

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

African (AFR) AF: 0.0476 AC: 1977 AN: 41512

American (AMR) AF: 0.0791 AC: 1209 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.124 AC: 430 AN: 3472

East Asian (EAS) AF: 0.0531 AC: 274 AN: 5160

South Asian (SAS) AF: 0.117 AC: 564 AN: 4814

European-Finnish (FIN) AF: 0.0845 AC: 894 AN: 10578

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8520 AN: 67958

Other (OTH) AF: 0.0970 AC: 205 AN: 2114

Alfa AF: 0.113 Hom.: 1330

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
PhyloP100		-0.092
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17328707; hg19: chr6-41159153;