rs143389794
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_004070.4(CLCNKA):āc.1500C>Gā(p.Pro500Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,460,812 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. P500P) has been classified as Likely benign.
Frequency
Consequence
NM_004070.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLCNKA | NM_004070.4 | c.1500C>G | p.Pro500Pro | synonymous_variant | 15/20 | ENST00000331433.5 | NP_004061.3 | |
CLCNKA | NM_001042704.2 | c.1500C>G | p.Pro500Pro | synonymous_variant | 15/20 | NP_001036169.1 | ||
CLCNKA | NM_001257139.2 | c.1371C>G | p.Pro457Pro | synonymous_variant | 14/19 | NP_001244068.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLCNKA | ENST00000331433.5 | c.1500C>G | p.Pro500Pro | synonymous_variant | 15/20 | 1 | NM_004070.4 | ENSP00000332771.4 | ||
CLCNKA | ENST00000375692.5 | c.1500C>G | p.Pro500Pro | synonymous_variant | 16/21 | 1 | ENSP00000364844.1 | |||
CLCNKA | ENST00000439316.6 | c.1371C>G | p.Pro457Pro | synonymous_variant | 14/19 | 2 | ENSP00000414445.2 | |||
CLCNKA | ENST00000464764.5 | n.2104C>G | non_coding_transcript_exon_variant | 19/24 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000400 AC: 1AN: 250238Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135644
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1460812Hom.: 0 Cov.: 33 AF XY: 0.00000413 AC XY: 3AN XY: 726706
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at