NM_025140.3:c.-59-12969G>A

Variant names:

• chr12-123957333-C-T
• rs7305864
• NM_025140.3:c.-59-12969G>A

Variant summary

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

The NM_025140.3(CCDC92):​c.-59-12969G>A 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)
• Consequence: CCDC92 NM_025140.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.454
• Publications: 12 publications found

Genes affected

CCDC92 (HGNC:29563): (coiled-coil domain containing 92) Enables identical protein binding activity. Located in centriole; centrosome; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.86).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_025140.3. 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
	CCDC92	NM_025140.3	MANE Select	c.-59-12969G>A		intron	N/A	NP_079416.1	Q53HC0-1
	CCDC92	NM_001304957.2		c.-49-12979G>A		intron	N/A	NP_001291886.1	Q53HC0-1
	CCDC92	NM_001304958.2		c.-156-11533G>A		intron	N/A	NP_001291887.1	Q53HC0-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC92	ENST00000238156.8	TSL:1 MANE Select	c.-59-12969G>A		intron	N/A	ENSP00000238156.3	Q53HC0-1
	CCDC92	ENST00000902169.1		c.-59-12969G>A		intron	N/A	ENSP00000572228.1
	CCDC92	ENST00000902170.1		c.-49-12979G>A		intron	N/A	ENSP00000572229.1

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.84
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7305864; hg19: chr12-124441880;