NM_001134848.2:c.-50C>T

Variant names:

• chr5-42756838-C-T
• rs3797310
• NM_001134848.2:c.-50C>T

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.889
• Publications: 18 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.371 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC152	NM_001134848.2	MANE Select	c.-50C>T		5_prime_UTR	Exon 1 of 9	NP_001128320.1	Q4G0S7-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC152	ENST00000361970.10	TSL:1 MANE Select	c.-50C>T		5_prime_UTR	Exon 1 of 9	ENSP00000354888.5	Q4G0S7-1
	CCDC152	ENST00000927601.1		c.-294C>T		5_prime_UTR	Exon 1 of 10	ENSP00000597660.1
	CCDC152	ENST00000927600.1		c.-50C>T		5_prime_UTR	Exon 1 of 8	ENSP00000597659.1

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39391 AN: 151948 Hom.: 5695 Cov.: 32

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.: 37 Cov.: 0 AF XY: 0.348 AC XY: 144 AN XY: 414

African (AFR) AF: 0.00 AC: 0 AN: 8

American (AMR) AF: 0.333 AC: 2 AN: 6

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2

East Asian (EAS) AF: 0.167 AC: 1 AN: 6

South Asian (SAS) AF: 0.500 AC: 2 AN: 4

European-Finnish (FIN) AF: 0.349 AC: 150 AN: 430

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.347 AC: 66 AN: 190

Other (OTH) AF: 0.357 AC: 5 AN: 14

GnomAD4 genome AF: 0.259 AC: 39433 AN: 152066 Hom.: 5705 Cov.: 32 AF XY: 0.262 AC XY: 19440 AN XY: 74334

African (AFR) AF: 0.141 AC: 5850 AN: 41474

American (AMR) AF: 0.379 AC: 5791 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 974 AN: 3470

East Asian (EAS) AF: 0.280 AC: 1442 AN: 5156

South Asian (SAS) AF: 0.225 AC: 1088 AN: 4828

European-Finnish (FIN) AF: 0.347 AC: 3669 AN: 10568

Middle Eastern (MID) AF: 0.188 AC: 55 AN: 292

European-Non Finnish (NFE) AF: 0.291 AC: 19779 AN: 67976

Other (OTH) AF: 0.256 AC: 541 AN: 2110

Alfa AF: 0.278 Hom.: 3596

Bravo AF: 0.256

Asia WGS AF: 0.240 AC: 837 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.69
PhyloP100		-0.89
PromoterAI		0.10	Neutral
Mutation Taster		=300/0	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: rs3797310; hg19: chr5-42756940; COSMIC: COSV62794837;