6-31732311-G-T

Position:

• chr6-31732311-G-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_001288.6(CLIC1):​c.470C>A​(p.Ala157Asp) variant causes a missense 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: 31)
• Consequence: CLIC1 NM_001288.6 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.13

Genes affected

CLIC1 (HGNC:2062): (chloride intracellular channel 1) Chloride channels are a diverse group of proteins that regulate fundamental cellular processes including stabilization of cell membrane potential, transepithelial transport, maintenance of intracellular pH, and regulation of cell volume. Chloride intracellular channel 1 is a member of the p64 family; the protein localizes principally to the cell nucleus and exhibits both nuclear and plasma membrane chloride ion channel activity. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.29566717).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CLIC1	NM_001288.6	c.470C>A	p.Ala157Asp	missense_variant	5/6	ENST00000375784.8	NP_001279.2
CLIC1	NM_001287593.1	c.470C>A	p.Ala157Asp	missense_variant	6/7		NP_001274522.1
CLIC1	NM_001287594.3	c.470C>A	p.Ala157Asp	missense_variant	6/7		NP_001274523.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CLIC1	ENST00000375784.8	c.470C>A	p.Ala157Asp	missense_variant	5/6	1	NM_001288.6	ENSP00000364940.3

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Sep 04, 2024

The c.470C>A (p.A157D) alteration is located in exon 5 (coding exon 5) of the CLIC1 gene. This alteration results from a C to A substitution at nucleotide position 470, causing the alanine (A) at amino acid position 157 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Uncertain	0.15	D
BayesDel_noAF	Uncertain	-0.020
CADD	Benign	23
DANN	Benign	0.96
DEOGEN2	Benign	0.23	T;T;T;T;T
Eigen	Benign	0.013
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.94	D
M_CAP	Uncertain	0.10	D
MetaRNN	Benign	0.30	T;T;T;T;T
MetaSVM	Uncertain	0.049	D
MutationAssessor	Benign	1.4	L;L;L;L;L
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-2.0	N;N;N;N;.
REVEL	Uncertain	0.41
Sift	Benign	0.67	T;T;T;T;.
Sift4G	Benign	0.68	T;T;T;T;T
Polyphen		0.42	B;B;B;B;B
Vest4		0.43
MutPred		0.43		Gain of phosphorylation at T155 (P = 0.1115);Gain of phosphorylation at T155 (P = 0.1115);Gain of phosphorylation at T155 (P = 0.1115);Gain of phosphorylation at T155 (P = 0.1115);Gain of phosphorylation at T155 (P = 0.1115);
MVP		0.97
MPC		0.92
ClinPred		0.48	T
GERP RS		6.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.72
gMVP		0.71

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr6-31700088;