chr14-94288427-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_001100607.3(SERPINA10):c.851G>A(p.Arg284His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000039 in 1,613,958 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001100607.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA10 | NM_001100607.3 | c.851G>A | p.Arg284His | missense_variant | 3/5 | ENST00000261994.9 | |
SERPINA10 | NM_016186.3 | c.851G>A | p.Arg284His | missense_variant | 3/5 | ||
SERPINA10 | XM_017021353.2 | c.971G>A | p.Arg324His | missense_variant | 4/6 | ||
SERPINA10 | XM_005267733.6 | c.851G>A | p.Arg284His | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA10 | ENST00000261994.9 | c.851G>A | p.Arg284His | missense_variant | 3/5 | 1 | NM_001100607.3 | A2 | |
SERPINA10 | ENST00000554723.5 | c.971G>A | p.Arg324His | missense_variant | 3/5 | 1 | P4 | ||
SERPINA10 | ENST00000393096.5 | c.851G>A | p.Arg284His | missense_variant | 3/5 | 1 | A2 | ||
SERPINA10 | ENST00000554173.1 | c.851G>A | p.Arg284His | missense_variant | 2/4 | 1 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000395 AC: 6AN: 152070Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251434Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135878
GnomAD4 exome AF: 0.0000390 AC: 57AN: 1461888Hom.: 0 Cov.: 32 AF XY: 0.0000454 AC XY: 33AN XY: 727244
GnomAD4 genome AF: 0.0000395 AC: 6AN: 152070Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74276
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 15, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at