7-143756463-T-C
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_178561.5(CTAGE6):c.1196A>G(p.Tyr399Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000866 in 1,605,990 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_178561.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1196A>G | p.Tyr399Cys | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1196A>G | p.Tyr399Cys | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+12635A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000218 AC: 33AN: 151548Hom.: 2 Cov.: 25
GnomAD3 exomes AF: 0.000225 AC: 56AN: 248904Hom.: 1 AF XY: 0.000193 AC XY: 26AN XY: 134996
GnomAD4 exome AF: 0.0000729 AC: 106AN: 1454324Hom.: 2 Cov.: 31 AF XY: 0.0000705 AC XY: 51AN XY: 723528
GnomAD4 genome ? AF: 0.000218 AC: 33AN: 151666Hom.: 2 Cov.: 25 AF XY: 0.000310 AC XY: 23AN XY: 74182
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2021 | The c.1196A>G (p.Y399C) alteration is located in exon 1 (coding exon 1) of the CTAGE6 gene. This alteration results from a A to G substitution at nucleotide position 1196, causing the tyrosine (Y) at amino acid position 399 to be replaced by a cysteine (C). 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