rs1713456
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007110.5(TEP1):c.4403G>A(p.Cys1468Tyr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.192 in 1,613,728 control chromosomes in the GnomAD database, including 32,302 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 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 nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_007110.5 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 |
---|---|---|---|---|---|---|---|
TEP1 | NM_007110.5 | c.4403G>A | p.Cys1468Tyr | missense_variant | 30/55 | ENST00000262715.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEP1 | ENST00000262715.10 | c.4403G>A | p.Cys1468Tyr | missense_variant | 30/55 | 1 | NM_007110.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.245 AC: 37290AN: 151912Hom.: 5396 Cov.: 32
GnomAD3 exomes AF: 0.197 AC: 49396AN: 250592Hom.: 5500 AF XY: 0.194 AC XY: 26277AN XY: 135432
GnomAD4 exome AF: 0.186 AC: 272410AN: 1461698Hom.: 26895 Cov.: 35 AF XY: 0.186 AC XY: 135353AN XY: 727168
GnomAD4 genome ? AF: 0.246 AC: 37331AN: 152030Hom.: 5407 Cov.: 32 AF XY: 0.243 AC XY: 18051AN XY: 74342
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at