chr7-143756406-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_178561.5(CTAGE6):c.1253A>G(p.Lys418Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000255 in 1,605,980 control chromosomes in the GnomAD database, including 60 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 Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CTAGE6 | NM_178561.5 | c.1253A>G | p.Lys418Arg | missense_variant | 1/1 | ENST00000470691.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CTAGE6 | ENST00000470691.2 | c.1253A>G | p.Lys418Arg | missense_variant | 1/1 | NM_178561.5 | P1 | ||
ENST00000700950.1 | n.178+12692A>G | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000377 AC: 57AN: 151360Hom.: 2 Cov.: 25
GnomAD3 exomes AF: 0.000112 AC: 28AN: 249008Hom.: 4 AF XY: 0.000141 AC XY: 19AN XY: 135044
GnomAD4 exome AF: 0.000243 AC: 353AN: 1454504Hom.: 58 Cov.: 31 AF XY: 0.000240 AC XY: 174AN XY: 723508
GnomAD4 genome ? AF: 0.000376 AC: 57AN: 151476Hom.: 2 Cov.: 25 AF XY: 0.000365 AC XY: 27AN XY: 74068
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | The c.1253A>G (p.K418R) 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 1253, causing the lysine (K) at amino acid position 418 to be replaced by an arginine (R). 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