chr3-36546284-A-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_003149.3(STAC):āc.1204A>Cā(p.Ile402Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,866 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_003149.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
STAC | NM_003149.3 | c.1204A>C | p.Ile402Leu | missense_variant | 11/11 | ENST00000273183.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
STAC | ENST00000273183.8 | c.1204A>C | p.Ile402Leu | missense_variant | 11/11 | 1 | NM_003149.3 | P1 | |
STAC | ENST00000457375.6 | c.1021A>C | p.Ile341Leu | missense_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152204Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.0000319 AC: 8AN: 250966Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135626
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461544Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 727074
GnomAD4 genome AF: 0.000197 AC: 30AN: 152322Hom.: 1 Cov.: 32 AF XY: 0.000134 AC XY: 10AN XY: 74482
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.1204A>C (p.I402L) alteration is located in exon 11 (coding exon 11) of the STAC gene. This alteration results from a A to C substitution at nucleotide position 1204, causing the isoleucine (I) at amino acid position 402 to be replaced by a leucine (L). 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