1-24771754-T-A

Variant names:

• chr1-24771754-T-A
• rs9332415
• NM_013943.3:c.73-25988T>A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_013943.3(CLIC4):​c.73-25988T>A variant causes a intron 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CLIC4 NM_013943.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.11
• Publications: 8 publications found

Genes affected

CLIC4 (HGNC:13518): (chloride intracellular channel 4) 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 4 (CLIC4) protein, encoded by the CLIC4 gene, is a member of the p64 family; the gene is expressed in many tissues and exhibits a intracellular vesicular pattern in Panc-1 cells (pancreatic cancer cells). [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CLIC4	NM_013943.3	c.73-25988T>A		intron_variant	Intron 1 of 5	ENST00000374379.9	NP_039234.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CLIC4	ENST00000374379.9	c.73-25988T>A		intron_variant	Intron 1 of 5	1	NM_013943.3	ENSP00000363500.4
CLIC4	ENST00000488683.1	n.73-25988T>A		intron_variant	Intron 1 of 6	2		ENSP00000436538.1
CLIC4	ENST00000489758.1	n.218-25988T>A		intron_variant	Intron 1 of 1	2
CLIC4	ENST00000497755.1	n.245-21423T>A		intron_variant	Intron 1 of 5	3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 242872 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 142070

African (AFR) AF: 0.00 AC: 0 AN: 6710

American (AMR) AF: 0.00 AC: 0 AN: 19780

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 7232

East Asian (EAS) AF: 0.00 AC: 0 AN: 9002

South Asian (SAS) AF: 0.00 AC: 0 AN: 45932

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 13132

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2486

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 127446

Other (OTH) AF: 0.00 AC: 0 AN: 11152

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 6792

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	14
DANN	Benign	0.90
PhyloP100		1.1
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs9332415; hg19: chr1-25098245;