NM_016403.4:c.561-463G>T

Variant names:

• chr11-94963977-C-A
• rs7937776
• NM_016403.4:c.561-463G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_016403.4(CWC15):​c.561-463G>T 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: 29)
• Consequence: CWC15 NM_016403.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 6 publications found

Genes affected

CWC15 (HGNC:26939): (CWC15 spliceosome associated protein homolog) Predicted to enable RNA binding activity. Involved in mRNA splicing, via spliceosome. Located in mitochondrion and nuclear speck. Part of U2-type catalytic step 2 spliceosome. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000299714 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CWC15	NM_016403.4	c.561-463G>T		intron_variant	Intron 6 of 6	ENST00000279839.8	NP_057487.2
CWC15	NM_001363371.2	c.561-463G>T		intron_variant	Intron 6 of 6		NP_001350300.1
CWC15	NM_001363372.2	c.561-463G>T		intron_variant	Intron 6 of 6		NP_001350301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CWC15	ENST00000279839.8	c.561-463G>T		intron_variant	Intron 6 of 6	1	NM_016403.4	ENSP00000475615.2
CWC15	ENST00000616442.4	n.387-463G>T		intron_variant	Intron 2 of 2	2
CWC15	ENST00000621358.4	n.967-463G>T		intron_variant	Intron 5 of 5	5
ENSG00000299714	ENST00000765796.1	n.135+3608C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 29

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

GnomAD4 genome Cov.: 29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.41
PhyloP100		-0.13

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: rs7937776; hg19: chr11-94697142;