2-119465857-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_002980.3(SCTR):c.435G>A(p.Met145Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,930 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_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.435G>A | p.Met145Ile | missense_variant | 5/13 | ENST00000019103.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCTR | ENST00000019103.8 | c.435G>A | p.Met145Ile | missense_variant | 5/13 | 1 | NM_002980.3 | P1 | |
SCTR | ENST00000627145.1 | c.510G>A | p.Met170Ile | missense_variant | 6/8 | 5 | |||
SCTR | ENST00000630739.2 | c.231G>A | p.Met77Ile | missense_variant | 6/8 | 5 | |||
SCTR | ENST00000485440.1 | n.1184-1602G>A | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000398 AC: 10AN: 251390Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135864
GnomAD4 exome AF: 0.000124 AC: 181AN: 1461766Hom.: 0 Cov.: 30 AF XY: 0.000116 AC XY: 84AN XY: 727194
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74348
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 20, 2023 | The c.435G>A (p.M145I) alteration is located in exon 5 (coding exon 5) of the SCTR gene. This alteration results from a G to A substitution at nucleotide position 435, causing the methionine (M) at amino acid position 145 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