chr15-89584319-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_152259.4(TICRR):c.968C>A(p.Thr323Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,980 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TICRR | NM_152259.4 | c.968C>A | p.Thr323Asn | missense_variant | 3/22 | ENST00000268138.12 | |
TICRR | NM_001308025.1 | c.965C>A | p.Thr322Asn | missense_variant | 3/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TICRR | ENST00000268138.12 | c.968C>A | p.Thr323Asn | missense_variant | 3/22 | 5 | NM_152259.4 | A2 | |
TICRR | ENST00000560985.5 | c.965C>A | p.Thr322Asn | missense_variant | 3/22 | 1 | P4 | ||
ENST00000559041.1 | n.48-7184C>A | intron_variant, non_coding_transcript_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000854 AC: 13AN: 152160Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000362 AC: 9AN: 248838Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135048
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461820Hom.: 0 Cov.: 31 AF XY: 0.0000110 AC XY: 8AN XY: 727210
GnomAD4 genome ? AF: 0.0000854 AC: 13AN: 152160Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.968C>A (p.T323N) alteration is located in exon 3 (coding exon 3) of the TICRR gene. This alteration results from a C to A substitution at nucleotide position 968, causing the threonine (T) at amino acid position 323 to be replaced by an asparagine (N). 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