chr11-2402689-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005706.4(TSSC4):c.56C>T(p.Thr19Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,587,182 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005706.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TSSC4 | NM_005706.4 | c.56C>T | p.Thr19Met | missense_variant | 3/3 | ENST00000333256.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TSSC4 | ENST00000333256.11 | c.56C>T | p.Thr19Met | missense_variant | 3/3 | 1 | NM_005706.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000118 AC: 18AN: 152168Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000444 AC: 9AN: 202498Hom.: 0 AF XY: 0.0000459 AC XY: 5AN XY: 108862
GnomAD4 exome AF: 0.0000286 AC: 41AN: 1435014Hom.: 0 Cov.: 30 AF XY: 0.0000295 AC XY: 21AN XY: 711252
GnomAD4 genome AF: 0.000118 AC: 18AN: 152168Hom.: 0 Cov.: 33 AF XY: 0.000135 AC XY: 10AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 18, 2022 | The c.56C>T (p.T19M) alteration is located in exon 2 (coding exon 1) of the TSSC4 gene. This alteration results from a C to T substitution at nucleotide position 56, causing the threonine (T) at amino acid position 19 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