5-42769545-T-A

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001134848.2(CCDC152):​c.194-52T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.46).

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>A		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>A		intron	N/A	ENSP00000354888.5
	CCDC152	ENST00000388827.4	TSL:2	c.194-52T>A		intron	N/A	ENSP00000373479.4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1261520 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 619484

African (AFR) AF: 0.00 AC: 0 AN: 26196

American (AMR) AF: 0.00 AC: 0 AN: 17296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21424

East Asian (EAS) AF: 0.00 AC: 0 AN: 30866

South Asian (SAS) AF: 0.00 AC: 0 AN: 66030

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 41416

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4868

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1001942

Other (OTH) AF: 0.00 AC: 0 AN: 51482

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.46
CADD	Benign	16
DANN	Benign	0.73
PhyloP100		1.6

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;