11-124951679-T-C

Variant names:

• chr11-124951679-T-C
• rs4408325
• ENST00000649496.2:n.511-129A>G

Variant summary

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

The ENST00000649496.2(CCDC15-DT):​n.511-129A>G 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: 30)
• Consequence: CCDC15-DT ENST00000649496.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.115
• Publications: 10 publications found

Genes affected

CCDC15-DT (HGNC:54193): (CCDC15 divergent transcript)

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=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC15-DT	XR_948132.3	n.511-129A>G		intron_variant	Intron 1 of 2
CCDC15-DT	XR_948133.3	n.511-129A>G		intron_variant	Intron 1 of 2
CCDC15-DT	XR_948134.3	n.511-129A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC15-DT	ENST00000649496.2	n.511-129A>G		intron_variant	Intron 1 of 2
CCDC15-DT	ENST00000655771.2	n.564-129A>G		intron_variant	Intron 1 of 2
CCDC15-DT	ENST00000667169.2	n.48-129A>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

Alfa AF: 0.00 Hom.: 1247

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.4
DANN	Benign	0.55
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs4408325; hg19: chr11-124821575;