13-99554368-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_004800.3(TM9SF2):c.1553C>T(p.Thr518Met) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,066 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004800.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TM9SF2 | NM_004800.3 | c.1553C>T | p.Thr518Met | missense_variant | Exon 14 of 17 | ENST00000376387.5 | NP_004791.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TM9SF2 | ENST00000376387.5 | c.1553C>T | p.Thr518Met | missense_variant | Exon 14 of 17 | 1 | NM_004800.3 | ENSP00000365567.3 | ||
TM9SF2 | ENST00000642475.1 | c.1553C>T | p.Thr518Met | missense_variant | Exon 16 of 19 | ENSP00000493515.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251446Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135898
GnomAD4 exome AF: 0.0000260 AC: 38AN: 1461838Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 727218
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152228Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1553C>T (p.T518M) alteration is located in exon 14 (coding exon 14) of the TM9SF2 gene. This alteration results from a C to T substitution at nucleotide position 1553, causing the threonine (T) at amino acid position 518 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at