rs767144751
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The NM_001122752.2(SERPINI1):āc.473A>Gā(p.Asn158Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000745 in 1,611,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. N158K) 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 -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINI1 | NM_001122752.2 | c.473A>G | p.Asn158Ser | missense_variant | 3/9 | ENST00000446050.7 | |
SERPINI1 | NM_005025.5 | c.473A>G | p.Asn158Ser | missense_variant | 3/9 | ||
SERPINI1 | XM_017006618.3 | c.473A>G | p.Asn158Ser | missense_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINI1 | ENST00000446050.7 | c.473A>G | p.Asn158Ser | missense_variant | 3/9 | 1 | NM_001122752.2 | P1 | |
SERPINI1 | ENST00000295777.9 | c.473A>G | p.Asn158Ser | missense_variant | 3/9 | 1 | P1 | ||
SERPINI1 | ENST00000472747.2 | c.473A>G | p.Asn158Ser | missense_variant | 3/5 | 3 | |||
SERPINI1 | ENST00000472941.5 | c.473A>G | p.Asn158Ser | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000440 AC: 11AN: 249888Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135070
GnomAD4 exome AF: 0.00000685 AC: 10AN: 1458904Hom.: 0 Cov.: 30 AF XY: 0.00000551 AC XY: 4AN XY: 725972
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152334Hom.: 0 Cov.: 32 AF XY: 0.0000268 AC XY: 2AN XY: 74494
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2021 | The c.473A>G (p.N158S) alteration is located in exon 3 (coding exon 2) of the SERPINI1 gene. This alteration results from a A to G substitution at nucleotide position 473, causing the asparagine (N) at amino acid position 158 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Familial encephalopathy with neuroserpin inclusion bodies Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 27, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at