rs2871328
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_001080477.4(TENM3):c.1791T>A(p.Ser597=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000694 in 1,440,912 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. S597S) has been classified as Benign.
Frequency
Consequence
NM_001080477.4 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 |
---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.1791T>A | p.Ser597= | synonymous_variant | 10/28 | ENST00000511685.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.1791T>A | p.Ser597= | synonymous_variant | 10/28 | 5 | NM_001080477.4 | P1 | |
TENM3 | ENST00000502950.1 | n.178T>A | non_coding_transcript_exon_variant | 2/15 | 2 | ||||
TENM3 | ENST00000507737.1 | n.323T>A | non_coding_transcript_exon_variant | 1/2 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.94e-7 AC: 1AN: 1440912Hom.: 0 Cov.: 36 AF XY: 0.00 AC XY: 0AN XY: 715238
GnomAD4 genome ? Cov.: 31
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at