14-94563894-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006215.4(SERPINA4):c.412C>T(p.Arg138Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000569 in 1,614,172 control chromosomes in the GnomAD database, including 3 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_006215.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SERPINA4 | NM_006215.4 | c.412C>T | p.Arg138Cys | missense_variant | 2/5 | ENST00000557004.6 | |
SERPINA4 | NM_001289032.2 | c.523C>T | p.Arg175Cys | missense_variant | 2/5 | ||
SERPINA4 | NM_001289033.2 | c.412C>T | p.Arg138Cys | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SERPINA4 | ENST00000557004.6 | c.412C>T | p.Arg138Cys | missense_variant | 2/5 | 1 | NM_006215.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00279 AC: 424AN: 152162Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000939 AC: 236AN: 251446Hom.: 1 AF XY: 0.000765 AC XY: 104AN XY: 135888
GnomAD4 exome AF: 0.000339 AC: 495AN: 1461892Hom.: 1 Cov.: 33 AF XY: 0.000327 AC XY: 238AN XY: 727246
GnomAD4 genome AF: 0.00278 AC: 424AN: 152280Hom.: 2 Cov.: 33 AF XY: 0.00278 AC XY: 207AN XY: 74448
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Apr 20, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at