CCDC121 p.Arg154Arg

Variant names:

• chr2-27627823-G-G
• NM_024584.5:c.

Your query was ambiguous. Multiple possible variants found:

• chr2-27627824--
• chr2-27627826-T-G
• chr2-27627824-C-T
• chr2-27627824-CCT-ACG
• chr2-27627824-CCT-GCG
• chr2-27627824-CCT-TCG

Variant summary

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

The NM_001142683.3(CCDC121):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CCDC121 NM_001142683.3 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.79
• Publications: 0 publications found

Genes affected

CCDC121 (HGNC:25833): (coiled-coil domain containing 121)

ENSG00000259080 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142683.3. 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
	CCDC121	NM_024584.5	MANE Select	c.		exon_region	Exon 2 of 2	NP_078860.2
	CCDC121	NM_024584.5	MANE Select	c.		5_prime_UTR	Exon 2 of 2	NP_078860.2
	CCDC121	NM_001142683.3		c.		exon_region	Exon 2 of 2	NP_001136155.1	Q6ZUS5-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC121	ENST00000324364.4	TSL:1 MANE Select	c.		exon_region	Exon 2 of 2	ENSP00000339087.2	Q6ZUS5-1
	CCDC121	ENST00000394775.3	TSL:1	c.		exon_region	Exon 2 of 2	ENSP00000412150.2	Q6ZUS5-2
	CCDC121	ENST00000324364.4	TSL:1 MANE Select	c.		5_prime_UTR	Exon 2 of 2	ENSP00000339087.2	Q6ZUS5-1

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
PhyloP100		-3.8

Splicing

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: chr2-27850690;