1-86486743-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001285.4(CLCA1):c.1172C>T(p.Ser391Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000143 in 1,613,838 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001285.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLCA1 | NM_001285.4 | c.1172C>T | p.Ser391Leu | missense_variant | 7/14 | ENST00000394711.2 | NP_001276.3 | |
LOC124904210 | XR_007066206.1 | n.226-5935G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLCA1 | ENST00000394711.2 | c.1172C>T | p.Ser391Leu | missense_variant | 7/14 | 1 | NM_001285.4 | ENSP00000378200.1 | ||
CLCA1 | ENST00000234701.7 | c.1172C>T | p.Ser391Leu | missense_variant | 8/15 | 1 | ENSP00000234701.3 |
Frequencies
GnomAD3 genomes AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000796 AC: 2AN: 251104Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135722
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461654Hom.: 0 Cov.: 34 AF XY: 0.00000963 AC XY: 7AN XY: 727128
GnomAD4 genome AF: 0.0000657 AC: 10AN: 152184Hom.: 0 Cov.: 33 AF XY: 0.0000942 AC XY: 7AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 31, 2023 | The c.1172C>T (p.S391L) alteration is located in exon 7 (coding exon 7) of the CLCA1 gene. This alteration results from a C to T substitution at nucleotide position 1172, causing the serine (S) at amino acid position 391 to be replaced by a leucine (L). 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