CCDC30 p.Met345Ile

Variant names:

• chr1-42556300-G-T
• NM_001395517.1:c.1035G>T
• CCDC30 p.Met345Ile

Your query was ambiguous. Multiple possible variants found:

• chr1-42556300-G-T
• chr1-42556300-G-C
• chr1-42556300-G-A

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001395517.1(CCDC30):​c.1035G>T​(p.Met345Ile) variant causes a missense 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. 16/22 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC30 NM_001395517.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.81
• Publications: 0 publications found

Genes affected

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

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.08784443).

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.1035G>T	p.Met345Ile	missense	Exon 10 of 21	NP_001382446.1	A0A590UK19
	CCDC30	NM_001080850.4		c.570G>T	p.Met190Ile	missense	Exon 6 of 17	NP_001074319.1	Q5VVM6-1
	CCDC30	NM_001355224.2		c.-475G>T		5_prime_UTR	Exon 11 of 23	NP_001342153.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC30	ENST00000657597.2	MANE Select	c.1035G>T	p.Met345Ile	missense	Exon 10 of 21	ENSP00000499662.2	A0A590UK19
	CCDC30	ENST00000514642.1	TSL:1	c.28-9996G>T		intron	N/A	ENSP00000499505.1	A0A590UJL6
	CCDC30	ENST00000477155.6	TSL:1	n.*975G>T		non_coding_transcript_exon	Exon 11 of 23	ENSP00000421479.3	D6RFH8

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.19
BayesDel_addAF	Benign	-0.33	T
BayesDel_noAF	Benign	-0.71
CADD	Benign	15
DANN	Benign	0.76
DEOGEN2	Benign	0.0019	T
Eigen	Benign	-0.61
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.62	D
LIST_S2	Benign	0.47	T
M_CAP	Benign	0.0059	T
MetaRNN	Benign	0.088	T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.90	L
PhyloP100		1.8
PrimateAI	Benign	0.24	T
PROVEAN	Benign	-0.74	N
REVEL	Benign	0.045
Sift	Benign	0.49	T
Sift4G	Benign	0.50	T
Varity_R		0.057
gMVP		0.038
Mutation Taster		=97/3	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr1-43021971;