14-94496502-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001382267.1(SERPINA12):c.776T>C(p.Ile259Thr) variant causes a missense change. The variant allele was found at a frequency of 0.0000248 in 1,614,002 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I259L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001382267.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA12 | NM_001382267.1 | c.776T>C | p.Ile259Thr | missense_variant | 3/5 | ENST00000677451.1 | |
SERPINA12 | NM_001304461.2 | c.776T>C | p.Ile259Thr | missense_variant | 3/5 | ||
SERPINA12 | NM_173850.4 | c.776T>C | p.Ile259Thr | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA12 | ENST00000677451.1 | c.776T>C | p.Ile259Thr | missense_variant | 3/5 | NM_001382267.1 | P1 | ||
SERPINA12 | ENST00000341228.2 | c.776T>C | p.Ile259Thr | missense_variant | 4/6 | 1 | P1 | ||
SERPINA12 | ENST00000556881.5 | c.776T>C | p.Ile259Thr | missense_variant | 3/5 | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251358Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135840
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461848Hom.: 0 Cov.: 32 AF XY: 0.0000316 AC XY: 23AN XY: 727218
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 06, 2021 | The c.776T>C (p.I259T) alteration is located in exon 4 (coding exon 2) of the SERPINA12 gene. This alteration results from a T to C substitution at nucleotide position 776, causing the isoleucine (I) at amino acid position 259 to be replaced by a threonine (T). 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