Genetic Variant CCDC152:c.-50C>T (chr5-42756838-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001134848.2(CCDC152):c.-50C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.26 in 152,726 control chromosomes in the GnomAD database, including 5,742 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 0.26 ( 5705 hom., cov: 32)

Exomes 𝑓: 0.34 ( 37 hom. )

Consequence

CCDC152
NM_001134848.2 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.889

Variant links:

Genes affected

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

CCDC152 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC152	NM_001134848.2 link	c.-50C>T		5_prime_UTR_variant	Exon 1 of 9	ENST00000361970.10	NP_001128320.1	Q4G0S7-1A0A024R043
CCDC152	XM_047416584.1 link	c.-388C>T		5_prime_UTR_variant	Exon 1 of 9		XP_047272540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC152	ENST00000361970 link	c.-50C>T		5_prime_UTR_variant	Exon 1 of 9	1	NM_001134848.2	ENSP00000354888.5		Q4G0S7-1
CCDC152	ENST00000388827 link	c.-50C>T		5_prime_UTR_variant	Exon 1 of 7	2		ENSP00000373479.4		Q4G0S7-2

Frequencies

GnomAD3 genomes

AF:

0.259

AC:

39391

AN:

151948

Hom.:

5695

Cov.:

show subpopulations

Gnomad AFR

AF:

0.141

Gnomad AMI

AF:

0.268

Gnomad AMR

AF:

0.379

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.278

Gnomad SAS

AF:

0.225

Gnomad FIN

AF:

0.347

Gnomad MID

AF:

0.172

Gnomad NFE

AF:

0.291

Gnomad OTH

AF:

0.251

GnomAD4 exome

AF:

0.342

AC:

226

AN:

660

Hom.:

Cov.:

AF XY:

0.348

AC XY:

144

AN XY:

414

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.333

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.167

Gnomad4 SAS exome

AF:

0.500

Gnomad4 FIN exome

AF:

0.349

Gnomad4 NFE exome

AF:

0.347

Gnomad4 OTH exome

AF:

0.357

GnomAD4 genome

AF:

0.259

AC:

39433

AN:

152066

Hom.:

5705

Cov.:

AF XY:

0.262

AC XY:

19440

AN XY:

74334

show subpopulations

Gnomad4 AFR

AF:

0.141

Gnomad4 AMR

AF:

0.379

Gnomad4 ASJ

AF:

0.281

Gnomad4 EAS

AF:

0.280

Gnomad4 SAS

AF:

0.225

Gnomad4 FIN

AF:

0.347

Gnomad4 NFE

AF:

0.291

Gnomad4 OTH

AF:

0.256

Alfa

AF:

0.280

Hom.:

2236

Bravo

AF:

0.256

Asia WGS

AF:

0.240

AC:

837

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

3.4

DANN

Benign

0.69

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over