rs7107185

Variant names:

• chr11-94969885-T-A
• rs7107185
• NM_016403.4:c.441+104A>T

Your query was ambiguous. Multiple possible variants found:

• chr11-94969885-T-A
• chr11-94969885-T-C

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.441+104A>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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CWC15 NM_016403.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 7 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=-0.88).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CWC15	NM_016403.4	c.441+104A>T		intron_variant	Intron 5 of 6	ENST00000279839.8	NP_057487.2
CWC15	NM_001363371.2	c.441+104A>T		intron_variant	Intron 5 of 6		NP_001350300.1
CWC15	NM_001363372.2	c.441+104A>T		intron_variant	Intron 5 of 6		NP_001350301.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CWC15	ENST00000279839.8	c.441+104A>T		intron_variant	Intron 5 of 6	1	NM_016403.4	ENSP00000475615.2
CWC15	ENST00000616442.4	n.267+104A>T		intron_variant	Intron 1 of 2	2
CWC15	ENST00000621358.4	n.847+104A>T		intron_variant	Intron 4 of 5	5
ENSG00000299714	ENST00000765796.1	n.136-149T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 424614 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 220198

African (AFR) AF: 0.00 AC: 0 AN: 10284

American (AMR) AF: 0.00 AC: 0 AN: 10914

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11848

East Asian (EAS) AF: 0.00 AC: 0 AN: 26302

South Asian (SAS) AF: 0.00 AC: 0 AN: 24952

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 31664

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 1742

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 283590

Other (OTH) AF: 0.00 AC: 0 AN: 23318

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 2714

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.61
DANN	Benign	0.40
PhyloP100		-1.5

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: rs7107185; hg19: chr11-94703049;