6-41158653-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000338469.3(TREM2):c.610A>G(p.Thr204Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000685 in 1,605,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/12 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000338469.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TREM2 | NM_018965.4 | c.*111A>G | 3_prime_UTR_variant | 5/5 | ENST00000373113.8 | ||
TREM2 | NM_001271821.2 | c.610A>G | p.Thr204Ala | missense_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TREM2 | ENST00000338469.3 | c.610A>G | p.Thr204Ala | missense_variant | 4/4 | 1 | |||
TREM2 | ENST00000373113.8 | c.*111A>G | 3_prime_UTR_variant | 5/5 | 1 | NM_018965.4 | P1 | ||
TREM2 | ENST00000373122.8 | c.*175A>G | 3_prime_UTR_variant | 5/5 | 1 | ||||
ENST00000702590.1 | n.364+3090T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000128 AC: 3AN: 234744Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 126380
GnomAD4 exome AF: 0.00000688 AC: 10AN: 1453296Hom.: 0 Cov.: 31 AF XY: 0.00000970 AC XY: 7AN XY: 721946
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152052Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74294
ClinVar
Submissions by phenotype
Polycystic lipomembranous osteodysplasia with sclerosing leukoencephalopathy 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at