rs1117707

Positions:

• chr5-65093838-A-G
• chr5-65093838-A-T

Variant summary

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

The XR_001742681.2(LOC107986419):​n.191-5414A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,876 control chromosomes in the GnomAD database, including 8,719 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 0.33 (8719 hom., cov: 31)
• Consequence: LOC107986419 XR_001742681.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04

Genes affected

LOC107986419 (HGNC:):

CWC27 (HGNC:10664): (CWC27 spliceosome associated cyclophilin) Predicted to enable peptidyl-prolyl cis-trans isomerase activity. Predicted to be involved in protein peptidyl-prolyl isomerization. Located in nucleoplasm. Part of U2-type precatalytic spliceosome and catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986419	XR_001742681.2	n.191-5414A>G		intron_variant, non_coding_transcript_variant
LOC107986419	XR_001742682.2	n.188-5414A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CWC27	ENST00000693303.1	c.1153-5414A>G		intron_variant				ENSP00000508557

Frequencies

GnomAD3 genomes AF: 0.334 AC: 50671 AN: 151758 Hom.: 8702 Cov.: 31

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.340

Gnomad SAS AF: 0.410

Gnomad FIN AF: 0.291

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.313

Gnomad OTH AF: 0.307

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

GnomAD4 genome AF: 0.334 AC: 50720 AN: 151876 Hom.: 8719 Cov.: 31 AF XY: 0.334 AC XY: 24761 AN XY: 74226

Gnomad4 AFR AF: 0.347

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.340

Gnomad4 SAS AF: 0.409

Gnomad4 FIN AF: 0.291

Gnomad4 NFE AF: 0.313

Gnomad4 OTH AF: 0.305

Alfa AF: 0.196 Hom.: 395

Bravo AF: 0.338

Asia WGS AF: 0.377 AC: 1310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1117707; hg19: chr5-64389665;