chr1-117623757-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong
The NM_017709.4(TENT5C):c.889G>A(p.Ala297Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00223 in 1,614,138 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).
Frequency
Consequence
NM_017709.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENT5C | NM_017709.4 | c.889G>A | p.Ala297Thr | missense_variant | 2/2 | ENST00000369448.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENT5C | ENST00000369448.4 | c.889G>A | p.Ala297Thr | missense_variant | 2/2 | 1 | NM_017709.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00152 AC: 231AN: 152130Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00153 AC: 385AN: 251318Hom.: 1 AF XY: 0.00155 AC XY: 210AN XY: 135830
GnomAD4 exome AF: 0.00230 AC: 3366AN: 1461890Hom.: 5 Cov.: 35 AF XY: 0.00225 AC XY: 1634AN XY: 727248
GnomAD4 genome ? AF: 0.00152 AC: 231AN: 152248Hom.: 0 Cov.: 31 AF XY: 0.00148 AC XY: 110AN XY: 74434
ClinVar
Submissions by phenotype
not specified Other:1
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at