13-23756604-C-T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1
The NM_005932.4(MIPEP):c.1985G>A(p.Arg662His) variant causes a missense change. The variant allele was found at a frequency of 0.000208 in 1,613,302 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R662C) has been classified as Uncertain significance.
Frequency
Consequence
NM_005932.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MIPEP | NM_005932.4 | c.1985G>A | p.Arg662His | missense_variant | 18/19 | ENST00000382172.4 | |
MIPEP | XM_011535097.3 | c.1799G>A | p.Arg600His | missense_variant | 18/19 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIPEP | ENST00000382172.4 | c.1985G>A | p.Arg662His | missense_variant | 18/19 | 1 | NM_005932.4 | P1 | |
MIPEP | ENST00000433710.2 | n.178G>A | non_coding_transcript_exon_variant | 3/4 | 3 | ||||
MIPEP | ENST00000464194.3 | n.227G>A | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00108 AC: 165AN: 152210Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000335 AC: 84AN: 250630Hom.: 0 AF XY: 0.000214 AC XY: 29AN XY: 135550
GnomAD4 exome AF: 0.000116 AC: 170AN: 1460974Hom.: 0 Cov.: 30 AF XY: 0.000120 AC XY: 87AN XY: 726854
GnomAD4 genome ? AF: 0.00108 AC: 165AN: 152328Hom.: 0 Cov.: 33 AF XY: 0.00115 AC XY: 86AN XY: 74488
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 20, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at