rs12880583
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_007110.5(TEP1):āc.2978A>Gā(p.His993Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000373 in 1,608,848 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H993Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_007110.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TEP1 | NM_007110.5 | c.2978A>G | p.His993Arg | missense_variant | 20/55 | ENST00000262715.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEP1 | ENST00000262715.10 | c.2978A>G | p.His993Arg | missense_variant | 20/55 | 1 | NM_007110.5 | P1 | |
TEP1 | ENST00000556935.5 | c.2654A>G | p.His885Arg | missense_variant | 18/53 | 1 | |||
TEP1 | ENST00000555008.5 | c.1028A>G | p.His343Arg | missense_variant, NMD_transcript_variant | 8/43 | 1 | |||
TEP1 | ENST00000555727.5 | c.2978A>G | p.His993Arg | missense_variant, NMD_transcript_variant | 20/54 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000811 AC: 2AN: 246584Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133344
GnomAD4 exome AF: 0.00000343 AC: 5AN: 1456768Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 724516
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74300
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at