rs200676193
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBP7
The NM_000083.3(CLCN1):c.1605C>A(p.Ala535=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,468 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. A535A) has been classified as Likely benign.
Frequency
Consequence
NM_000083.3 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 | UniProt |
---|---|---|---|---|---|---|---|
CLCN1 | NM_000083.3 | c.1605C>A | p.Ala535= | synonymous_variant | 15/23 | ENST00000343257.7 | |
CLCN1 | NR_046453.2 | n.1560C>A | non_coding_transcript_exon_variant | 14/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCN1 | ENST00000343257.7 | c.1605C>A | p.Ala535= | synonymous_variant | 15/23 | 1 | NM_000083.3 | P4 | |
CLCN1 | ENST00000432192.6 | c.*890C>A | 3_prime_UTR_variant, NMD_transcript_variant | 15/23 | 1 | ||||
CLCN1 | ENST00000650516.2 | c.1605C>A | p.Ala535= | synonymous_variant | 15/23 | A2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251378Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135868
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461468Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 727052
GnomAD4 genome ? Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at