6-44282504-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_182539.4(TCTE1):c.902G>A(p.Arg301Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000089 in 1,606,542 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_182539.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCTE1 | ENST00000371505.5 | c.902G>A | p.Arg301Gln | missense_variant | Exon 4 of 5 | 1 | NM_182539.4 | ENSP00000360560.4 | ||
ENSG00000272442 | ENST00000505802.1 | n.312+8998C>T | intron_variant | Intron 1 of 9 | 2 | ENSP00000424257.1 | ||||
TMEM151B | ENST00000438774.2 | c.576+8998C>T | intron_variant | Intron 2 of 2 | 3 | ENSP00000409337.2 | ||||
TCTE1 | ENST00000371504.1 | c.388-2114G>A | intron_variant | Intron 1 of 1 | 3 | ENSP00000360559.1 |
Frequencies
GnomAD3 genomes AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000613 AC: 15AN: 244832Hom.: 0 AF XY: 0.0000829 AC XY: 11AN XY: 132724
GnomAD4 exome AF: 0.0000949 AC: 138AN: 1454320Hom.: 0 Cov.: 35 AF XY: 0.000104 AC XY: 75AN XY: 723714
GnomAD4 genome AF: 0.0000328 AC: 5AN: 152222Hom.: 0 Cov.: 32 AF XY: 0.0000403 AC XY: 3AN XY: 74368
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.902G>A (p.R301Q) alteration is located in exon 4 (coding exon 3) of the TCTE1 gene. This alteration results from a G to A substitution at nucleotide position 902, causing the arginine (R) at amino acid position 301 to be replaced by a glutamine (Q). 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