chr5-42798931-G-C

Position:

• chr5-42798931-G-C

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
CCDC152	NM_001134848.2	c.559-444G>C		intron_variant		ENST00000361970.10
CCDC152	XM_047416584.1	c.622-444G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC152	ENST00000361970.10	c.559-444G>C		intron_variant		1	NM_001134848.2	P1
CCDC152	ENST00000388827.4	c.391-444G>C		intron_variant		2

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

Gnomad4 AFR AF: 0.560

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.419

Gnomad4 SAS AF: 0.524

Gnomad4 FIN AF: 0.637

Gnomad4 NFE AF: 0.540

Gnomad4 OTH AF: 0.551

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

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

Other links and lift over

dbSNP: rs230813; hg19: chr5-42799033;