chr19-54070160-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001135686.3(TARM1):āc.659T>Cā(p.Val220Ala) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,551,328 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001135686.3 missense, splice_region
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 |
---|---|---|---|---|---|---|---|
TARM1 | NM_001135686.3 | c.659T>C | p.Val220Ala | missense_variant, splice_region_variant | 5/5 | ENST00000432826.2 | |
TARM1 | NM_001330650.1 | c.683T>C | p.Val228Ala | missense_variant, splice_region_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TARM1 | ENST00000432826.2 | c.659T>C | p.Val220Ala | missense_variant, splice_region_variant | 5/5 | 1 | NM_001135686.3 | P2 | |
TARM1 | ENST00000616041.4 | c.683T>C | p.Val228Ala | missense_variant, splice_region_variant | 5/5 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000261 AC: 4AN: 153362Hom.: 0 AF XY: 0.0000246 AC XY: 2AN XY: 81368
GnomAD4 exome AF: 0.0000122 AC: 17AN: 1399124Hom.: 1 Cov.: 31 AF XY: 0.0000174 AC XY: 12AN XY: 690072
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152204Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 14, 2023 | The c.659T>C (p.V220A) alteration is located in exon 5 (coding exon 5) of the TARM1 gene. This alteration results from a T to C substitution at nucleotide position 659, causing the valine (V) at amino acid position 220 to be replaced by an alanine (A). 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