rs7305864

Positions:

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

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC92	NM_025140.3	c.-59-12969G>C		intron_variant		ENST00000238156.8	NP_079416.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC92	ENST00000238156.8	c.-59-12969G>C		intron_variant		1	NM_025140.3	ENSP00000238156.3

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

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.296

Gnomad4 ASJ AF: 0.371

Gnomad4 EAS AF: 0.0945

Gnomad4 SAS AF: 0.224

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.337

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.3
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7305864; hg19: chr12-124441880;