3-44354792-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173826.4(TCAIM):c.10C>T(p.His4Tyr) 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 1,610,606 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H4P) has been classified as Likely benign.
Frequency
Consequence
NM_173826.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000987 AC: 15AN: 152010Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000161 AC: 4AN: 248464Hom.: 0 AF XY: 0.0000149 AC XY: 2AN XY: 134428
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1458596Hom.: 0 Cov.: 30 AF XY: 0.0000152 AC XY: 11AN XY: 725622
GnomAD4 genome AF: 0.0000987 AC: 15AN: 152010Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74228
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.10C>T (p.H4Y) alteration is located in exon 2 (coding exon 1) of the TCAIM gene. This alteration results from a C to T substitution at nucleotide position 10, causing the histidine (H) at amino acid position 4 to be replaced by a tyrosine (Y). 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