rs198414

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001286.5(CLCN6):​c.*545G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Consequence

CLCN6
NM_001286.5 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.22
Variant links:
Genes affected
CLCN6 (HGNC:2024): (chloride voltage-gated channel 6) This gene encodes a member of the voltage-dependent chloride channel protein family. Members of this family can function as either chloride channels or antiporters. This protein is primarily localized to late endosomes and functions as a chloride/proton antiporter. Alternate splicing results in both coding and non-coding variants. Additional alternately spliced variants have been described but their full-length structure is unknown. [provided by RefSeq, Mar 2012]
NPPA-AS1 (HGNC:37635): (NPPA antisense RNA 1)

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLCN6NM_001286.5 linkc.*545G>A 3_prime_UTR_variant Exon 23 of 23 ENST00000346436.11 NP_001277.2 P51797-1
CLCN6NM_001256959.2 linkc.*545G>A 3_prime_UTR_variant Exon 22 of 22 NP_001243888.2 P51797-6
NPPA-AS1NR_037806.1 linkn.450G>A non_coding_transcript_exon_variant Exon 1 of 4
CLCN6NR_046428.2 linkn.3211G>A non_coding_transcript_exon_variant Exon 23 of 23

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLCN6ENST00000346436.11 linkc.*545G>A 3_prime_UTR_variant Exon 23 of 23 1 NM_001286.5 ENSP00000234488.9 P51797-1
CLCN6ENST00000312413.10 linkc.*545G>A 3_prime_UTR_variant Exon 22 of 22 2 ENSP00000308367.7 P51797-6
CLCN6ENST00000400892.3 linkn.*1252-290G>A intron_variant Intron 23 of 26 3 ENSP00000496938.1 A0A3B3IRY0
CLCN6ENST00000446542.5 linkn.-249G>A upstream_gene_variant 1

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.77
DANN
Benign
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs198414; hg19: chr1-11900825; API