NM_001395517.1:c.1686-2521T>C

Variant names:

• chr1-42586800-T-C
• rs12408987
• NM_001395517.1:c.1686-2521T>C

Variant summary

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

The NM_001395517.1(CCDC30):​c.1686-2521T>C 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: 31)
• Consequence: CCDC30 NM_001395517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452
• Publications: 4 publications found

Genes affected

CCDC30 (HGNC:26103): (coiled-coil domain containing 30)

ENSG00000285728 (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=-0.91).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395517.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC30	NM_001395517.1	MANE Select	c.1686-2521T>C		intron	N/A	NP_001382446.1	A0A590UK19
	CCDC30	NM_001080850.4		c.1221-2521T>C		intron	N/A	NP_001074319.1	Q5VVM6-1
	CCDC30	NM_001395379.1		c.1128-2521T>C		intron	N/A	NP_001382308.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC30	ENST00000657597.2	MANE Select	c.1686-2521T>C		intron	N/A	ENSP00000499662.2	A0A590UK19
	CCDC30	ENST00000514642.1	TSL:1	c.573-2521T>C		intron	N/A	ENSP00000499505.1	A0A590UJL6
	CCDC30	ENST00000477155.6	TSL:1	n.*1764-2521T>C		intron	N/A	ENSP00000421479.3	D6RFH8

Frequencies

GnomAD3 genomes Cov.: 31

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

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 502

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.45

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: rs12408987; hg19: chr1-43052471;