rs57960711
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_017510.6(TMED9):āc.47C>Gā(p.Thr16Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0366 in 1,611,446 control chromosomes in the GnomAD database, including 1,266 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T16A) has been classified as Likely benign.
Frequency
Consequence
NM_017510.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TMED9 | NM_017510.6 | c.47C>G | p.Thr16Ser | missense_variant | 1/5 | ENST00000332598.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TMED9 | ENST00000332598.7 | c.47C>G | p.Thr16Ser | missense_variant | 1/5 | 1 | NM_017510.6 | P1 | |
TMED9 | ENST00000505521.1 | n.45C>G | non_coding_transcript_exon_variant | 1/2 | 2 | ||||
TMED9 | ENST00000507723.1 | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0372 AC: 5655AN: 152220Hom.: 117 Cov.: 33
GnomAD3 exomes AF: 0.0271 AC: 6526AN: 240502Hom.: 137 AF XY: 0.0266 AC XY: 3497AN XY: 131462
GnomAD4 exome AF: 0.0366 AC: 53359AN: 1459112Hom.: 1149 Cov.: 32 AF XY: 0.0355 AC XY: 25770AN XY: 725630
GnomAD4 genome ? AF: 0.0372 AC: 5664AN: 152334Hom.: 117 Cov.: 33 AF XY: 0.0361 AC XY: 2691AN XY: 74494
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at