5-42798931-G-C

Variant names:

• chr5-42798931-G-C
• rs230813
• NM_001134848.2:c.559-444G>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.559-444G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.554 in 152,002 control chromosomes in the GnomAD database, including 23,562 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 0.55 (23562 hom., cov: 32)
• Consequence: CCDC152 NM_001134848.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.391
• Publications: 9 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.591 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC152	NM_001134848.2	c.559-444G>C		intron_variant	Intron 7 of 8	ENST00000361970.10	NP_001128320.1
CCDC152	XM_047416584.1	c.622-444G>C		intron_variant	Intron 7 of 8		XP_047272540.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC152	ENST00000361970.10	c.559-444G>C		intron_variant	Intron 7 of 8	1	NM_001134848.2	ENSP00000354888.5
CCDC152	ENST00000388827.4	c.391-444G>C		intron_variant	Intron 5 of 6	2		ENSP00000373479.4

Frequencies

GnomAD3 genomes AF: 0.554 AC: 84155 AN: 151884 Hom.: 23512 Cov.: 32

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.633

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.419

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.637

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.548

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.554 AC: 84278 AN: 152002 Hom.: 23562 Cov.: 32 AF XY: 0.554 AC XY: 41182 AN XY: 74306

African (AFR) AF: 0.560 AC: 23190 AN: 41426

American (AMR) AF: 0.601 AC: 9179 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1903 AN: 3468

East Asian (EAS) AF: 0.419 AC: 2167 AN: 5170

South Asian (SAS) AF: 0.524 AC: 2530 AN: 4830

European-Finnish (FIN) AF: 0.637 AC: 6723 AN: 10558

Middle Eastern (MID) AF: 0.442 AC: 129 AN: 292

European-Non Finnish (NFE) AF: 0.540 AC: 36721 AN: 67964

Other (OTH) AF: 0.551 AC: 1161 AN: 2108

Alfa AF: 0.415 Hom.: 1088

Bravo AF: 0.551

Asia WGS AF: 0.464 AC: 1613 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.33
DANN	Benign	0.33
PhyloP100		-0.39
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: rs230813; hg19: chr5-42799033;