chr3-167789345-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_ModerateBP6_ModerateBS2
The NM_001122752.2(SERPINI1):c.217C>T(p.Arg73Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000514 in 1,614,004 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. R73H) has been classified as Likely benign.
Frequency
Consequence
NM_001122752.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINI1 | NM_001122752.2 | c.217C>T | p.Arg73Cys | missense_variant | 2/9 | ENST00000446050.7 | |
SERPINI1 | NM_005025.5 | c.217C>T | p.Arg73Cys | missense_variant | 2/9 | ||
SERPINI1 | XM_017006618.3 | c.217C>T | p.Arg73Cys | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINI1 | ENST00000446050.7 | c.217C>T | p.Arg73Cys | missense_variant | 2/9 | 1 | NM_001122752.2 | P1 | |
SERPINI1 | ENST00000295777.9 | c.217C>T | p.Arg73Cys | missense_variant | 2/9 | 1 | P1 | ||
SERPINI1 | ENST00000472747.2 | c.217C>T | p.Arg73Cys | missense_variant | 2/5 | 3 | |||
SERPINI1 | ENST00000472941.5 | c.217C>T | p.Arg73Cys | missense_variant | 2/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000256 AC: 39AN: 152186Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000677 AC: 17AN: 251220Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135794
GnomAD4 exome AF: 0.0000301 AC: 44AN: 1461818Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727208
GnomAD4 genome ? AF: 0.000256 AC: 39AN: 152186Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74344
ClinVar
Submissions by phenotype
Familial encephalopathy with neuroserpin inclusion bodies Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at