17-82324627-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003004.3(SECTM1):c.358G>A(p.Val120Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,612,500 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_003004.3 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 |
---|---|---|---|---|---|---|---|
SECTM1 | NM_003004.3 | c.358G>A | p.Val120Met | missense_variant | 3/5 | ENST00000269389.8 | |
SECTM1 | XM_005256392.4 | c.358G>A | p.Val120Met | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SECTM1 | ENST00000269389.8 | c.358G>A | p.Val120Met | missense_variant | 3/5 | 1 | NM_003004.3 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000593 AC: 9AN: 151690Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 250854Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135594
GnomAD4 exome AF: 0.00000958 AC: 14AN: 1460810Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 726532
GnomAD4 genome ? AF: 0.0000593 AC: 9AN: 151690Hom.: 0 Cov.: 31 AF XY: 0.0000270 AC XY: 2AN XY: 74054
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.358G>A (p.V120M) alteration is located in exon 3 (coding exon 2) of the SECTM1 gene. This alteration results from a G to A substitution at nucleotide position 358, causing the valine (V) at amino acid position 120 to be replaced by a methionine (M). 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