chr5-42769545-T-C

Variant names:

• chr5-42769545-T-C
• rs12055266
• NM_001134848.2:c.194-52T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 15 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001134848.2. 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
	CCDC152	NM_001134848.2	MANE Select	c.194-52T>C		intron	N/A	NP_001128320.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC152	ENST00000361970.10	TSL:1 MANE Select	c.194-52T>C		intron	N/A	ENSP00000354888.5
	CCDC152	ENST00000388827.4	TSL:2	c.194-52T>C		intron	N/A	ENSP00000373479.4

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

African (AFR) AF: 0.0505 AC: 1322 AN: 26184

American (AMR) AF: 0.407 AC: 7010 AN: 17218

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 5328 AN: 21370

East Asian (EAS) AF: 0.299 AC: 9209 AN: 30780

South Asian (SAS) AF: 0.205 AC: 13506 AN: 65884

European-Finnish (FIN) AF: 0.328 AC: 13538 AN: 41300

Middle Eastern (MID) AF: 0.165 AC: 800 AN: 4860

European-Non Finnish (NFE) AF: 0.271 AC: 271006 AN: 1000228

Other (OTH) AF: 0.241 AC: 12376 AN: 51400

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

African (AFR) AF: 0.0608 AC: 2524 AN: 41510

American (AMR) AF: 0.347 AC: 5308 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 864 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1346 AN: 5168

South Asian (SAS) AF: 0.200 AC: 968 AN: 4828

European-Finnish (FIN) AF: 0.332 AC: 3468 AN: 10460

Middle Eastern (MID) AF: 0.126 AC: 37 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18053 AN: 67942

Other (OTH) AF: 0.215 AC: 454 AN: 2114

Alfa AF: 0.234 Hom.: 632

Bravo AF: 0.214

Asia WGS AF: 0.220 AC: 762 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	16
DANN	Benign	0.80
PhyloP100		1.6
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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