rs9395152

chr6-46083098-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370650.1(CLIC5):c.-45-2811T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.16 in 152,268 control chromosomes in the GnomAD database, including 2,204 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 0.16 (2204 hom., cov: 33)
• Consequence: CLIC5 NM_001370650.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.88

Genes affected

CLIC5 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CLIC5	NM_001370649.1	c.-55+46406T>C		intron_variant
CLIC5	NM_001370650.1	c.-45-2811T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24407 AN: 152150 Hom.: 2201 Cov.: 33

Gnomad AFR AF: 0.128

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.154

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.155

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.160 AC: 24429 AN: 152268 Hom.: 2204 Cov.: 33 AF XY: 0.163 AC XY: 12168 AN XY: 74470

Gnomad4 AFR AF: 0.128

Gnomad4 AMR AF: 0.136

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.154

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.160

Alfa AF: 0.167 Hom.: 1200

Bravo AF: 0.153

Asia WGS AF: 0.331 AC: 1150 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.026
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9395152; hg19: chr6-46050835;