11-627131-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021920.4(SCT):c.13C>T(p.Pro5Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000956 in 1,087,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021920.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCT | NM_021920.4 | c.13C>T | p.Pro5Ser | missense_variant | 1/4 | ENST00000176195.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCT | ENST00000176195.4 | c.13C>T | p.Pro5Ser | missense_variant | 1/4 | 1 | NM_021920.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000868 AC: 13AN: 149840Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000971 AC: 91AN: 937396Hom.: 0 Cov.: 18 AF XY: 0.000113 AC XY: 50AN XY: 441472
GnomAD4 genome AF: 0.0000867 AC: 13AN: 149952Hom.: 0 Cov.: 32 AF XY: 0.000109 AC XY: 8AN XY: 73206
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 28, 2023 | The c.13C>T (p.P5S) alteration is located in exon 1 (coding exon 1) of the SCT gene. This alteration results from a C to T substitution at nucleotide position 13, causing the proline (P) at amino acid position 5 to be replaced by a serine (S). 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