6-44286190-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The ENST00000371505.5(TCTE1):c.620G>A(p.Arg207Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,611,516 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
ENST00000371505.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TCTE1 | NM_182539.4 | c.620G>A | p.Arg207Gln | missense_variant | 3/5 | ENST00000371505.5 | NP_872345.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TCTE1 | ENST00000371505.5 | c.620G>A | p.Arg207Gln | missense_variant | 3/5 | 1 | NM_182539.4 | ENSP00000360560 | P1 | |
TCTE1 | ENST00000371504.1 | c.161G>A | p.Arg54Gln | missense_variant | 1/2 | 3 | ENSP00000360559 | |||
TMEM151B | ENST00000438774.2 | c.576+12684C>T | intron_variant | 3 | ENSP00000409337 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249492Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134990
GnomAD4 exome AF: 6.85e-7 AC: 1AN: 1459304Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 725670
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152212Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74362
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 01, 2023 | The c.620G>A (p.R207Q) alteration is located in exon 3 (coding exon 2) of the TCTE1 gene. This alteration results from a G to A substitution at nucleotide position 620, causing the arginine (R) at amino acid position 207 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