16-3015643-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021195.5(CLDN6):āc.379A>Gā(p.Ile127Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,613,162 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_021195.5 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 | UniProt |
---|---|---|---|---|---|---|---|
CLDN6 | NM_021195.5 | c.379A>G | p.Ile127Val | missense_variant | 2/2 | ENST00000328796.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLDN6 | ENST00000328796.5 | c.379A>G | p.Ile127Val | missense_variant | 2/2 | 1 | NM_021195.5 | P1 | |
CLDN6 | ENST00000396925.1 | c.379A>G | p.Ile127Val | missense_variant | 3/3 | 5 | P1 | ||
CLDN6 | ENST00000572154.1 | c.93+286A>G | intron_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000400 AC: 10AN: 250048Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135550
GnomAD4 exome AF: 0.0000103 AC: 15AN: 1460990Hom.: 0 Cov.: 35 AF XY: 0.0000110 AC XY: 8AN XY: 726806
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152172Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74352
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.379A>G (p.I127V) alteration is located in exon 2 (coding exon 1) of the CLDN6 gene. This alteration results from a A to G substitution at nucleotide position 379, causing the isoleucine (I) at amino acid position 127 to be replaced by a valine (V). 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