9-120997683-C-T
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001735.3(C5):c.2654G>A(p.Arg885His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000295 in 1,614,102 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict 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. R885C) has been classified as Uncertain significance.
Frequency
Consequence
NM_001735.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C5 | NM_001735.3 | c.2654G>A | p.Arg885His | missense_variant | 21/41 | ENST00000223642.3 | |
C5 | NM_001317163.2 | c.2672G>A | p.Arg891His | missense_variant | 21/41 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C5 | ENST00000223642.3 | c.2654G>A | p.Arg885His | missense_variant | 21/41 | 1 | NM_001735.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.000210 AC: 32AN: 152118Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000326 AC: 82AN: 251480Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135916
GnomAD4 exome AF: 0.000304 AC: 444AN: 1461866Hom.: 4 Cov.: 32 AF XY: 0.000287 AC XY: 209AN XY: 727232
GnomAD4 genome AF: 0.000210 AC: 32AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.000282 AC XY: 21AN XY: 74436
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2023 | - - |
Eculizumab, poor response to Other:1
Affects, no assertion criteria provided | literature only | OMIM | Feb 13, 2014 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at