rs1760897
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_007110.5(TEP1):āc.346T>Cā(p.Ser116Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.324 in 1,613,824 control chromosomes in the GnomAD database, including 87,221 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 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. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S116C) has been classified as Uncertain significance.
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.346T>C | p.Ser116Pro | missense_variant | 2/55 | ENST00000262715.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TEP1 | ENST00000262715.10 | c.346T>C | p.Ser116Pro | missense_variant | 2/55 | 1 | NM_007110.5 | P1 | |
TEP1 | ENST00000556935.5 | c.346T>C | p.Ser116Pro | missense_variant | 2/53 | 1 | |||
TEP1 | ENST00000555727.5 | c.346T>C | p.Ser116Pro | missense_variant, NMD_transcript_variant | 2/54 | 1 | |||
TEP1 | ENST00000556549.1 | c.346T>C | p.Ser116Pro | missense_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.365 AC: 55381AN: 151832Hom.: 10817 Cov.: 31
GnomAD3 exomes AF: 0.331 AC: 83278AN: 251460Hom.: 14589 AF XY: 0.329 AC XY: 44741AN XY: 135902
GnomAD4 exome AF: 0.320 AC: 467312AN: 1461874Hom.: 76379 Cov.: 54 AF XY: 0.321 AC XY: 233328AN XY: 727236
GnomAD4 genome AF: 0.365 AC: 55436AN: 151950Hom.: 10842 Cov.: 31 AF XY: 0.362 AC XY: 26872AN XY: 74252
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at