2-119461901-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002980.3(SCTR):āc.736A>Gā(p.Ile246Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,672 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 (ā ).
Frequency
Consequence
NM_002980.3 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 |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.736A>G | p.Ile246Val | missense_variant | 7/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.736A>G | p.Ile246Val | missense_variant | 7/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000485440.1 | n.1416A>G | non_coding_transcript_exon_variant | 4/10 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000395 AC: 6AN: 152034Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250974Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135640
GnomAD4 exome AF: 0.0000397 AC: 58AN: 1461638Hom.: 0 Cov.: 31 AF XY: 0.0000316 AC XY: 23AN XY: 727110
GnomAD4 genome ? AF: 0.0000395 AC: 6AN: 152034Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 07, 2022 | The c.736A>G (p.I246V) alteration is located in exon 7 (coding exon 7) of the SCTR gene. This alteration results from a A to G substitution at nucleotide position 736, causing the isoleucine (I) at amino acid position 246 to be replaced by a valine (V). 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