chr3-111567553-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005816.5(CD96):c.449C>T(p.Thr150Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000252 in 1,602,838 control chromosomes in the GnomAD database, including 1 homozygotes. 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 Likely benign (★).
Frequency
Consequence
NM_005816.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD96 | NM_005816.5 | c.449C>T | p.Thr150Met | missense_variant | 3/14 | ENST00000352690.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD96 | ENST00000352690.9 | c.449C>T | p.Thr150Met | missense_variant | 3/14 | 1 | NM_005816.5 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000565 AC: 86AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000482 AC: 121AN: 251196Hom.: 0 AF XY: 0.000420 AC XY: 57AN XY: 135768
GnomAD4 exome AF: 0.000219 AC: 318AN: 1450750Hom.: 1 Cov.: 27 AF XY: 0.000220 AC XY: 159AN XY: 722532
GnomAD4 genome ? AF: 0.000565 AC: 86AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.000915 AC XY: 68AN XY: 74298
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 19, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at