rs2234258
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 4P and 16B. PVS1_StrongBP6_Very_StrongBS1BS2
The NM_001271821.2(TREM2):c.572G>A(p.Trp191*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.002 in 1,614,028 control chromosomes in the GnomAD database, including 39 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001271821.2 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TREM2 | ENST00000338469.3 | c.572G>A | p.Trp191* | stop_gained | Exon 4 of 4 | 1 | ENSP00000342651.4 | |||
TREM2 | ENST00000373113 | c.*73G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | NM_018965.4 | ENSP00000362205.3 | |||
TREM2 | ENST00000373122 | c.*137G>A | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000362214.4 | ||||
ENSG00000290034 | ENST00000702590.1 | n.364+3128C>T | intron_variant | Intron 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.0104 AC: 1579AN: 152144Hom.: 21 Cov.: 32
GnomAD3 exomes AF: 0.00306 AC: 768AN: 250988Hom.: 6 AF XY: 0.00243 AC XY: 329AN XY: 135664
GnomAD4 exome AF: 0.00114 AC: 1661AN: 1461766Hom.: 19 Cov.: 31 AF XY: 0.00101 AC XY: 738AN XY: 727172
GnomAD4 genome AF: 0.0103 AC: 1575AN: 152262Hom.: 20 Cov.: 32 AF XY: 0.00973 AC XY: 724AN XY: 74438
ClinVar
Submissions by phenotype
not provided Benign:5
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See Variant Classification Assertion Criteria. -
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TREM2: BS1, BS2 -
not specified Benign:1
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Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 2 Benign:1
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at