rs116929575
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_001085.5(SERPINA3):āc.1240A>Gā(p.Met414Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000735 in 1,614,118 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_001085.5 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 |
---|---|---|---|---|---|---|---|
SERPINA3 | NM_001085.5 | c.1240A>G | p.Met414Val | missense_variant | 5/5 | ENST00000393078.5 | |
SERPINA3 | NM_001384672.1 | c.1240A>G | p.Met414Val | missense_variant | 5/5 | ||
SERPINA3 | NM_001384673.1 | c.1240A>G | p.Met414Val | missense_variant | 6/6 | ||
SERPINA3 | NM_001384674.1 | c.1240A>G | p.Met414Val | missense_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA3 | ENST00000393078.5 | c.1240A>G | p.Met414Val | missense_variant | 5/5 | 1 | NM_001085.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000394 AC: 60AN: 152118Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.000855 AC: 215AN: 251458Hom.: 3 AF XY: 0.000773 AC XY: 105AN XY: 135906
GnomAD4 exome AF: 0.000771 AC: 1127AN: 1461882Hom.: 19 Cov.: 31 AF XY: 0.000744 AC XY: 541AN XY: 727242
GnomAD4 genome ? AF: 0.000388 AC: 59AN: 152236Hom.: 1 Cov.: 32 AF XY: 0.000390 AC XY: 29AN XY: 74426
ClinVar
Submissions by phenotype
ANTICHYMOTRYPSIN ISEHARA 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2001 | - - |
Peripheral arterial occlusive disease 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | reference population | Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center | Mar 18, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at