rs2227289
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_016579.4(CD320):c.837C>T(p.Thr279=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000248 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. T279T) has been classified as Benign.
Frequency
Consequence
NM_016579.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD320 | NM_016579.4 | c.837C>T | p.Thr279= | synonymous_variant | 5/5 | ENST00000301458.10 | |
CD320 | NM_001165895.2 | c.711C>T | p.Thr237= | synonymous_variant | 4/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD320 | ENST00000301458.10 | c.837C>T | p.Thr279= | synonymous_variant | 5/5 | 1 | NM_016579.4 | P1 | |
CD320 | ENST00000596002.5 | c.*1125C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 1 | ||||
CD320 | ENST00000537716.6 | c.711C>T | p.Thr237= | synonymous_variant | 4/4 | 2 | |||
CD320 | ENST00000599573.1 | c.*437C>T | 3_prime_UTR_variant, NMD_transcript_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152116Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251384Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135886
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461832Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727214
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152234Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74446
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at