5-42769545-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001134848.2(CCDC152):c.194-52T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 1,411,194 control chromosomes in the GnomAD database, including 50,444 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 0.22 (4520 hom., cov: 32)
  • Exomes 𝑓: 0.27 (45924 hom.)
• Consequence: CCDC152 NM_001134848.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.60

Genes affected

CCDC152 (HGNC:34438): (coiled-coil domain containing 152)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.34 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC152	NM_001134848.2	c.194-52T>C		intron_variant		ENST00000361970.10
CCDC152	XM_047416584.1	c.257-52T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC152	ENST00000361970.10	c.194-52T>C		intron_variant		1	NM_001134848.2	P1
CCDC152	ENST00000388827.4	c.194-52T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33189 AN: 151852 Hom.: 4510 Cov.: 32

Gnomad AFR AF: 0.0609

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.200

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.209

GnomAD4 exome AF: 0.265 AC: 334095 AN: 1259224 Hom.: 45924 AF XY: 0.263 AC XY: 162915 AN XY: 618326

Gnomad4 AFR exome AF: 0.0505

Gnomad4 AMR exome AF: 0.407

Gnomad4 ASJ exome AF: 0.249

Gnomad4 EAS exome AF: 0.299

Gnomad4 SAS exome AF: 0.205

Gnomad4 FIN exome AF: 0.328

Gnomad4 NFE exome AF: 0.271

Gnomad4 OTH exome AF: 0.241

GnomAD4 genome AF: 0.219 AC: 33227 AN: 151970 Hom.: 4520 Cov.: 32 AF XY: 0.222 AC XY: 16508 AN XY: 74326

Gnomad4 AFR AF: 0.0608

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.249

Gnomad4 EAS AF: 0.260

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.266

Gnomad4 OTH AF: 0.215

Alfa AF: 0.240 Hom.: 627

Bravo AF: 0.214

Asia WGS AF: 0.220 AC: 762 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	16
Dann	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs12055266; hg19: chr5-42769647; COSMIC: COSV62793658;