chrX-65716828-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP3BP6_ModerateBS2
The NM_002444.3(MSN):c.23G>A(p.Arg8His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000215 in 1,206,923 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 8 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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. R8C) has been classified as Uncertain significance.
Frequency
Consequence
NM_002444.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MSN | NM_002444.3 | c.23G>A | p.Arg8His | missense_variant | 2/13 | ENST00000360270.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MSN | ENST00000360270.7 | c.23G>A | p.Arg8His | missense_variant | 2/13 | 1 | NM_002444.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000274 AC: 3AN: 109469Hom.: 0 Cov.: 21 AF XY: 0.0000315 AC XY: 1AN XY: 31757
GnomAD3 exomes AF: 0.0000328 AC: 6AN: 182896Hom.: 0 AF XY: 0.0000445 AC XY: 3AN XY: 67478
GnomAD4 exome AF: 0.0000210 AC: 23AN: 1097454Hom.: 0 Cov.: 29 AF XY: 0.0000193 AC XY: 7AN XY: 362864
GnomAD4 genome AF: 0.0000274 AC: 3AN: 109469Hom.: 0 Cov.: 21 AF XY: 0.0000315 AC XY: 1AN XY: 31757
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 10, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at