chr2-119461980-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_002980.3(SCTR):āc.657G>Cā(p.Met219Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000747 in 1,606,720 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_002980.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCTR | NM_002980.3 | c.657G>C | p.Met219Ile | missense_variant | 7/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.657G>C | p.Met219Ile | missense_variant | 7/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000485440.1 | n.1337G>C | non_coding_transcript_exon_variant | 4/10 | 2 | ||||
SCTR | ENST00000627145.1 | downstream_gene_variant | 5 | ||||||
SCTR | ENST00000630739.2 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000123 AC: 3AN: 243938Hom.: 0 AF XY: 0.0000152 AC XY: 2AN XY: 131860
GnomAD4 exome AF: 0.00000619 AC: 9AN: 1454414Hom.: 0 Cov.: 31 AF XY: 0.00000415 AC XY: 3AN XY: 723300
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74472
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.657G>C (p.M219I) alteration is located in exon 7 (coding exon 7) of the SCTR gene. This alteration results from a G to C substitution at nucleotide position 657, causing the methionine (M) at amino acid position 219 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