2-119441584-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002980.3(SCTR):c.1156G>A(p.Val386Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,612,968 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_002980.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.1156G>A | p.Val386Ile | missense_variant | 12/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.1156G>A | p.Val386Ile | missense_variant | 12/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000485440.1 | n.1836G>A | non_coding_transcript_exon_variant | 9/10 | 2 | ||||
SCTR | ENST00000494326.5 | n.80G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152186Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249634Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 134800
GnomAD4 exome AF: 0.0000205 AC: 30AN: 1460664Hom.: 0 Cov.: 32 AF XY: 0.0000220 AC XY: 16AN XY: 726576
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74480
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2024 | The c.1156G>A (p.V386I) alteration is located in exon 12 (coding exon 12) of the SCTR gene. This alteration results from a G to A substitution at nucleotide position 1156, causing the valine (V) at amino acid position 386 to be replaced by an isoleucine (I). 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