chr3-167790461-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_ModerateBP6_Very_StrongBS2
The NM_001122752.2(SERPINI1):c.340G>A(p.Val114Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000774 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V114L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001122752.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINI1 | NM_001122752.2 | c.340G>A | p.Val114Met | missense_variant | 3/9 | ENST00000446050.7 | |
SERPINI1 | NM_005025.5 | c.340G>A | p.Val114Met | missense_variant | 3/9 | ||
SERPINI1 | XM_017006618.3 | c.340G>A | p.Val114Met | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINI1 | ENST00000446050.7 | c.340G>A | p.Val114Met | missense_variant | 3/9 | 1 | NM_001122752.2 | P1 | |
SERPINI1 | ENST00000295777.9 | c.340G>A | p.Val114Met | missense_variant | 3/9 | 1 | P1 | ||
SERPINI1 | ENST00000472747.2 | c.340G>A | p.Val114Met | missense_variant | 3/5 | 3 | |||
SERPINI1 | ENST00000472941.5 | c.340G>A | p.Val114Met | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.000394 AC: 60AN: 152188Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000836 AC: 21AN: 251344Hom.: 0 AF XY: 0.0000810 AC XY: 11AN XY: 135830
GnomAD4 exome AF: 0.0000445 AC: 65AN: 1461702Hom.: 0 Cov.: 31 AF XY: 0.0000399 AC XY: 29AN XY: 727156
GnomAD4 genome AF: 0.000394 AC: 60AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.000376 AC XY: 28AN XY: 74480
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 13, 2022 | 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. - |
SERPINI1-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 27, 2023 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Familial encephalopathy with neuroserpin inclusion bodies Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at