15-89584466-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_152259.4(TICRR):c.1115C>T(p.Ala372Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000484 in 1,610,540 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_152259.4 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 |
---|---|---|---|---|---|---|---|
TICRR | NM_152259.4 | c.1115C>T | p.Ala372Val | missense_variant | 3/22 | ENST00000268138.12 | |
TICRR | NM_001308025.1 | c.1112C>T | p.Ala371Val | missense_variant | 3/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICRR | ENST00000268138.12 | c.1115C>T | p.Ala372Val | missense_variant | 3/22 | 5 | NM_152259.4 | A2 | |
TICRR | ENST00000560985.5 | c.1112C>T | p.Ala371Val | missense_variant | 3/22 | 1 | P4 | ||
ENST00000559041.1 | n.48-7037C>T | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000250 AC: 38AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000731 AC: 18AN: 246220Hom.: 0 AF XY: 0.0000972 AC XY: 13AN XY: 133680
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1458236Hom.: 0 Cov.: 31 AF XY: 0.0000221 AC XY: 16AN XY: 725258
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000282 AC XY: 21AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.1115C>T (p.A372V) alteration is located in exon 3 (coding exon 3) of the TICRR gene. This alteration results from a C to T substitution at nucleotide position 1115, causing the alanine (A) at amino acid position 372 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