6-45957230-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_016929.5(CLIC5):​c.64-1986T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.837 in 151,756 control chromosomes in the GnomAD database, including 53,723 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 0.84 ( 53723 hom., cov: 32)

Consequence

CLIC5
NM_016929.5 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.231
Variant links:
Genes affected
CLIC5 (HGNC:13517): (chloride intracellular channel 5) This gene encodes a member of the chloride intracellular channel (CLIC) family of chloride ion channels. The encoded protein associates with actin-based cytoskeletal structures and may play a role in multiple processes including hair cell stereocilia formation, myoblast proliferation and glomerular podocyte and endothelial cell maintenance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Dec 2011]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.893 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CLIC5NM_016929.5 linkuse as main transcriptc.64-1986T>C intron_variant ENST00000339561.12

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CLIC5ENST00000339561.12 linkuse as main transcriptc.64-1986T>C intron_variant 1 NM_016929.5 P1Q9NZA1-2

Frequencies

GnomAD3 genomes
AF:
0.837
AC:
126952
AN:
151634
Hom.:
53681
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.775
Gnomad AMI
AF:
0.982
Gnomad AMR
AF:
0.829
Gnomad ASJ
AF:
0.900
Gnomad EAS
AF:
0.488
Gnomad SAS
AF:
0.732
Gnomad FIN
AF:
0.883
Gnomad MID
AF:
0.809
Gnomad NFE
AF:
0.898
Gnomad OTH
AF:
0.849
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.837
AC:
127056
AN:
151756
Hom.:
53723
Cov.:
32
AF XY:
0.831
AC XY:
61676
AN XY:
74192
show subpopulations
Gnomad4 AFR
AF:
0.775
Gnomad4 AMR
AF:
0.829
Gnomad4 ASJ
AF:
0.900
Gnomad4 EAS
AF:
0.488
Gnomad4 SAS
AF:
0.731
Gnomad4 FIN
AF:
0.883
Gnomad4 NFE
AF:
0.899
Gnomad4 OTH
AF:
0.846
Alfa
AF:
0.876
Hom.:
26640
Bravo
AF:
0.830
Asia WGS
AF:
0.644
AC:
2237
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.91
CADD
Benign
7.2
DANN
Benign
0.75

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: rs4714892; hg19: chr6-45924967; API