chr19-54074022-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001135686.3(TARM1):c.556G>A(p.Val186Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000657 in 1,551,678 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001135686.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TARM1 | NM_001135686.3 | c.556G>A | p.Val186Met | missense_variant | 4/5 | ENST00000432826.2 | |
TARM1 | NM_001330650.1 | c.580G>A | p.Val194Met | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TARM1 | ENST00000432826.2 | c.556G>A | p.Val186Met | missense_variant | 4/5 | 1 | NM_001135686.3 | P2 | |
TARM1 | ENST00000616041.4 | c.580G>A | p.Val194Met | missense_variant | 4/5 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152160Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000649 AC: 10AN: 154092Hom.: 0 AF XY: 0.0000489 AC XY: 4AN XY: 81762
GnomAD4 exome AF: 0.0000657 AC: 92AN: 1399400Hom.: 1 Cov.: 32 AF XY: 0.0000609 AC XY: 42AN XY: 690208
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152278Hom.: 0 Cov.: 31 AF XY: 0.0000403 AC XY: 3AN XY: 74442
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 05, 2024 | The c.556G>A (p.V186M) alteration is located in exon 4 (coding exon 4) of the TARM1 gene. This alteration results from a G to A substitution at nucleotide position 556, causing the valine (V) at amino acid position 186 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at