chr14-94289954-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001100607.3(SERPINA10):c.640C>T(p.Arg214Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000632 in 1,614,038 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 (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R214Q) has been classified as Likely benign.
Frequency
Consequence
NM_001100607.3 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 |
---|---|---|---|---|---|---|---|
SERPINA10 | NM_001100607.3 | c.640C>T | p.Arg214Trp | missense_variant | 2/5 | ENST00000261994.9 | |
SERPINA10 | NM_016186.3 | c.640C>T | p.Arg214Trp | missense_variant | 2/5 | ||
SERPINA10 | XM_017021353.2 | c.760C>T | p.Arg254Trp | missense_variant | 3/6 | ||
SERPINA10 | XM_005267733.6 | c.640C>T | p.Arg214Trp | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA10 | ENST00000261994.9 | c.640C>T | p.Arg214Trp | missense_variant | 2/5 | 1 | NM_001100607.3 | A2 | |
SERPINA10 | ENST00000554723.5 | c.760C>T | p.Arg254Trp | missense_variant | 2/5 | 1 | P4 | ||
SERPINA10 | ENST00000393096.5 | c.640C>T | p.Arg214Trp | missense_variant | 2/5 | 1 | A2 | ||
SERPINA10 | ENST00000554173.1 | c.640C>T | p.Arg214Trp | missense_variant | 1/4 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000915 AC: 23AN: 251386Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135898
GnomAD4 exome AF: 0.0000636 AC: 93AN: 1461858Hom.: 0 Cov.: 33 AF XY: 0.0000605 AC XY: 44AN XY: 727230
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152180Hom.: 0 Cov.: 33 AF XY: 0.0000404 AC XY: 3AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 03, 2022 | The c.640C>T (p.R214W) alteration is located in exon 2 (coding exon 1) of the SERPINA10 gene. This alteration results from a C to T substitution at nucleotide position 640, causing the arginine (R) at amino acid position 214 to be replaced by a tryptophan (W). 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