14-94288388-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001100607.3(SERPINA10):c.890C>T(p.Thr297Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00007 in 1,614,118 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001100607.3 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 |
---|---|---|---|---|---|---|---|
SERPINA10 | NM_001100607.3 | c.890C>T | p.Thr297Ile | missense_variant | 3/5 | ENST00000261994.9 | |
SERPINA10 | NM_016186.3 | c.890C>T | p.Thr297Ile | missense_variant | 3/5 | ||
SERPINA10 | XM_017021353.2 | c.1010C>T | p.Thr337Ile | missense_variant | 4/6 | ||
SERPINA10 | XM_005267733.6 | c.890C>T | p.Thr297Ile | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA10 | ENST00000261994.9 | c.890C>T | p.Thr297Ile | missense_variant | 3/5 | 1 | NM_001100607.3 | A2 | |
SERPINA10 | ENST00000554723.5 | c.1010C>T | p.Thr337Ile | missense_variant | 3/5 | 1 | P4 | ||
SERPINA10 | ENST00000393096.5 | c.890C>T | p.Thr297Ile | missense_variant | 3/5 | 1 | A2 | ||
SERPINA10 | ENST00000554173.1 | c.890C>T | p.Thr297Ile | missense_variant | 2/4 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.000105 AC: 16AN: 152122Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000676 AC: 17AN: 251446Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135886
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1461878Hom.: 0 Cov.: 32 AF XY: 0.0000756 AC XY: 55AN XY: 727234
GnomAD4 genome AF: 0.000105 AC: 16AN: 152240Hom.: 0 Cov.: 32 AF XY: 0.000107 AC XY: 8AN XY: 74424
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2023 | The c.890C>T (p.T297I) alteration is located in exon 3 (coding exon 2) of the SERPINA10 gene. This alteration results from a C to T substitution at nucleotide position 890, causing the threonine (T) at amino acid position 297 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