chr3-111567556-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_005816.5(CD96):c.452T>C(p.Ile151Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000404 in 1,605,074 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005816.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD96 | NM_005816.5 | c.452T>C | p.Ile151Thr | missense_variant | 3/14 | ENST00000352690.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD96 | ENST00000352690.9 | c.452T>C | p.Ile151Thr | missense_variant | 3/14 | 1 | NM_005816.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000230 AC: 35AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000167 AC: 42AN: 251180Hom.: 0 AF XY: 0.000184 AC XY: 25AN XY: 135760
GnomAD4 exome AF: 0.000422 AC: 613AN: 1452890Hom.: 0 Cov.: 27 AF XY: 0.000409 AC XY: 296AN XY: 723472
GnomAD4 genome ? AF: 0.000230 AC: 35AN: 152184Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74354
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 29, 2021 | The c.452T>C (p.I151T) alteration is located in exon 3 (coding exon 3) of the CD96 gene. This alteration results from a T to C substitution at nucleotide position 452, causing the isoleucine (I) at amino acid position 151 to be replaced by a threonine (T). 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