chr6-155276324-T-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001001346.3(CLDN20):āc.605T>Cā(p.Ile202Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,550 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_001001346.3 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 |
---|---|---|---|---|---|---|---|---|
CLDN20 | NM_001001346.3 | c.605T>C | p.Ile202Thr | missense_variant | 2/2 | ENST00000367165.3 | NP_001001346.1 | |
TFB1M | NM_016020.4 | c.666+8834A>G | intron_variant | ENST00000367166.5 | NP_057104.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLDN20 | ENST00000367165.3 | c.605T>C | p.Ile202Thr | missense_variant | 2/2 | 1 | NM_001001346.3 | ENSP00000356133 | P1 | |
TFB1M | ENST00000367166.5 | c.666+8834A>G | intron_variant | 1 | NM_016020.4 | ENSP00000356134 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248390Hom.: 0 AF XY: 0.00000741 AC XY: 1AN XY: 134914
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461462Hom.: 0 Cov.: 35 AF XY: 0.00000825 AC XY: 6AN XY: 727026
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74300
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 20, 2024 | The c.605T>C (p.I202T) alteration is located in exon 2 (coding exon 1) of the CLDN20 gene. This alteration results from a T to C substitution at nucleotide position 605, causing the isoleucine (I) at amino acid position 202 to be replaced by a threonine (T). 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