3-111585362-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PP3_ModeratePP5BS2
The NM_005816.5(CD96):c.791C>T(p.Thr264Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000261 in 1,607,772 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_005816.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD96 | NM_005816.5 | c.791C>T | p.Thr264Met | missense_variant | 5/14 | ENST00000352690.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD96 | ENST00000352690.9 | c.791C>T | p.Thr264Met | missense_variant | 5/14 | 1 | NM_005816.5 | P2 | |
CD96 | ENST00000283285.10 | c.839C>T | p.Thr280Met | missense_variant | 6/15 | 1 | A2 | ||
CD96 | ENST00000438817.6 | c.791C>T | p.Thr264Met | missense_variant | 5/8 | 1 | A2 | ||
CD96 | ENST00000494798.1 | c.791C>T | p.Thr264Met | missense_variant, NMD_transcript_variant | 5/15 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000239 AC: 6AN: 251402Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135874
GnomAD4 exome AF: 0.0000275 AC: 40AN: 1455724Hom.: 0 Cov.: 27 AF XY: 0.0000276 AC XY: 20AN XY: 724638
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152048Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
C syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 01, 2007 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at