rs2180762
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001285.4(CLCA1):c.304-22G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.961 in 1,556,322 control chromosomes in the GnomAD database, including 719,747 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.92 ( 65001 hom., cov: 33)
Exomes 𝑓: 0.97 ( 654746 hom. )
Consequence
CLCA1
NM_001285.4 intron
NM_001285.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.267
Genes affected
CLCA1 (HGNC:2015): (chloride channel accessory 1) This gene encodes a member of the calcium sensitive chloride conductance protein family. To date, all members of this gene family map to the same region on chromosome 1p31-p22 and share a high degree of homology in size, sequence, and predicted structure, but differ significantly in their tissue distributions. The encoded protein is expressed as a precursor protein that is processed into two cell-surface-associated subunits, although the site at which the precursor is cleaved has not been precisely determined. The encoded protein may be involved in mediating calcium-activated chloride conductance in the intestine. [provided by RefSeq, Jul 2008]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.964 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLCA1 | NM_001285.4 | c.304-22G>A | intron_variant | ENST00000394711.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLCA1 | ENST00000394711.2 | c.304-22G>A | intron_variant | 1 | NM_001285.4 | P1 | |||
CLCA1 | ENST00000234701.7 | c.304-22G>A | intron_variant | 1 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.922 AC: 140229AN: 152152Hom.: 64963 Cov.: 33
GnomAD3 genomes
?
AF:
AC:
140229
AN:
152152
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD3 exomes AF: 0.951 AC: 210143AN: 220932Hom.: 100181 AF XY: 0.953 AC XY: 114191AN XY: 119766
GnomAD3 exomes
AF:
AC:
210143
AN:
220932
Hom.:
AF XY:
AC XY:
114191
AN XY:
119766
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.965 AC: 1355301AN: 1404052Hom.: 654746 Cov.: 30 AF XY: 0.965 AC XY: 669070AN XY: 693116
GnomAD4 exome
AF:
AC:
1355301
AN:
1404052
Hom.:
Cov.:
30
AF XY:
AC XY:
669070
AN XY:
693116
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome ? AF: 0.922 AC: 140323AN: 152270Hom.: 65001 Cov.: 33 AF XY: 0.919 AC XY: 68399AN XY: 74452
GnomAD4 genome
?
AF:
AC:
140323
AN:
152270
Hom.:
Cov.:
33
AF XY:
AC XY:
68399
AN XY:
74452
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at