rs7305864

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr12-123957333-C-G
• chr12-123957333-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_025140.3(CCDC92):​c.-59-12969G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,126 control chromosomes in the GnomAD database, including 7,980 homozygotes. 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: 𝑓 0.32 (7980 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.339 is higher than 0.05.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC92	NM_025140.3	MANE Select	c.-59-12969G>C		intron	N/A	NP_079416.1
	CCDC92	NM_001304957.2		c.-49-12979G>C		intron	N/A	NP_001291886.1
	CCDC92	NM_001304958.2		c.-156-11533G>C		intron	N/A	NP_001291887.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC92	ENST00000238156.8	TSL:1 MANE Select	c.-59-12969G>C		intron	N/A	ENSP00000238156.3
	CCDC92	ENST00000545891.5	TSL:2	c.-17-13840G>C		intron	N/A	ENSP00000440024.1
	CCDC92	ENST00000539761.5	TSL:3	c.-228-11533G>C		intron	N/A	ENSP00000439441.1

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48695 AN: 152008 Hom.: 7973 Cov.: 32

Gnomad AFR AF: 0.343

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.371

Gnomad EAS AF: 0.0945

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.320 AC: 48734 AN: 152126 Hom.: 7980 Cov.: 32 AF XY: 0.313 AC XY: 23295 AN XY: 74372

African (AFR) AF: 0.344 AC: 14246 AN: 41468

American (AMR) AF: 0.296 AC: 4530 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.371 AC: 1286 AN: 3466

East Asian (EAS) AF: 0.0945 AC: 490 AN: 5184

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4828

European-Finnish (FIN) AF: 0.280 AC: 2963 AN: 10582

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.338 AC: 22949 AN: 67994

Other (OTH) AF: 0.337 AC: 711 AN: 2112

Alfa AF: 0.200 Hom.: 420

Bravo AF: 0.325

Asia WGS AF: 0.214 AC: 745 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.51
PhyloP100		0.45
Mutation Taster		=100/0	polymorphism (auto)

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;