chr5-181260602-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001346048.2(TRIM52):c.212C>T(p.Ala71Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000322 in 1,613,484 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001346048.2 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 |
---|---|---|---|---|---|---|---|
TRIM52 | NM_001346048.2 | c.212C>T | p.Ala71Val | missense_variant | 1/2 | ENST00000688015.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TRIM52 | ENST00000688015.1 | c.212C>T | p.Ala71Val | missense_variant | 1/2 | NM_001346048.2 | A2 | ||
CTC-338M12.4 | ENST00000511331.5 | n.632-10971G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000660 AC: 10AN: 151506Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250452Hom.: 0 AF XY: 0.0000591 AC XY: 8AN XY: 135454
GnomAD4 exome AF: 0.0000287 AC: 42AN: 1461860Hom.: 0 Cov.: 32 AF XY: 0.0000358 AC XY: 26AN XY: 727224
GnomAD4 genome AF: 0.0000660 AC: 10AN: 151624Hom.: 0 Cov.: 32 AF XY: 0.0000675 AC XY: 5AN XY: 74082
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2022 | The c.212C>T (p.A71V) alteration is located in exon 1 (coding exon 1) of the TRIM52 gene. This alteration results from a C to T substitution at nucleotide position 212, causing the alanine (A) at amino acid position 71 to be replaced by a valine (V). 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