NM_006999.6:c.1739C>T
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_006999.6(TENT4A):c.1739C>T(p.Thr580Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000136 in 1,612,896 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T580P) has been classified as Likely benign.
Frequency
Consequence
NM_006999.6 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENT4A | NM_006999.6 | c.1739C>T | p.Thr580Met | missense_variant | Exon 10 of 13 | ENST00000230859.8 | NP_008930.2 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 249726Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135062
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1460638Hom.: 0 Cov.: 31 AF XY: 0.0000165 AC XY: 12AN XY: 726638
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152258Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74376
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.989C>T (p.T330M) alteration is located in exon 10 (coding exon 9) of the PAPD7 gene. This alteration results from a C to T substitution at nucleotide position 989, causing the threonine (T) at amino acid position 330 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at