chr1-56912476-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_000562.3(C8A):c.1454G>A(p.Arg485His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00128 in 1,614,144 control chromosomes in the GnomAD database, including 10 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R485L) has been classified as Benign.
Frequency
Consequence
NM_000562.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C8A | NM_000562.3 | c.1454G>A | p.Arg485His | missense_variant | 10/11 | ENST00000361249.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C8A | ENST00000361249.4 | c.1454G>A | p.Arg485His | missense_variant | 10/11 | 1 | NM_000562.3 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00121 AC: 184AN: 152142Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00195 AC: 491AN: 251300Hom.: 4 AF XY: 0.00216 AC XY: 293AN XY: 135868
GnomAD4 exome AF: 0.00129 AC: 1883AN: 1461884Hom.: 10 Cov.: 33 AF XY: 0.00145 AC XY: 1052AN XY: 727244
GnomAD4 genome AF: 0.00121 AC: 184AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.00117 AC XY: 87AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at