chr8-27745683-G-A

Variant names:

• chr8-27745683-G-A
• rs17477326
• NM_018246.3:c.551+2394C>T

Variant summary

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

The NM_018246.3(CCDC25):​c.551+2394C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.3 in 152,100 control chromosomes in the GnomAD database, including 8,001 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 0.30 (8001 hom., cov: 33)
• Consequence: CCDC25 NM_018246.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 10 publications found

Genes affected

CCDC25 (HGNC:25591): (coiled-coil domain containing 25) Enables DNA binding activity. Involved in positive regulation of cell motility. Located in endomembrane system. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000253875 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018246.3. 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
	CCDC25	NM_018246.3	MANE Select	c.551+2394C>T		intron	N/A	NP_060716.2
	CCDC25	NM_001304532.2		c.347+2394C>T		intron	N/A	NP_001291461.1
	CCDC25	NM_001304530.2		c.347+2394C>T		intron	N/A	NP_001291459.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC25	ENST00000356537.9	TSL:1 MANE Select	c.551+2394C>T		intron	N/A	ENSP00000348933.4
	CCDC25	ENST00000520202.5	TSL:1	n.*266+2394C>T		intron	N/A	ENSP00000428587.1
	CCDC25	ENST00000520486.5	TSL:1	n.*370+2394C>T		intron	N/A	ENSP00000427714.1

Frequencies

GnomAD3 genomes AF: 0.300 AC: 45625 AN: 151982 Hom.: 8006 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.300 AC: 45642 AN: 152100 Hom.: 8001 Cov.: 33 AF XY: 0.304 AC XY: 22597 AN XY: 74334

African (AFR) AF: 0.124 AC: 5125 AN: 41496

American (AMR) AF: 0.311 AC: 4759 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1663 AN: 3468

East Asian (EAS) AF: 0.120 AC: 619 AN: 5160

South Asian (SAS) AF: 0.349 AC: 1681 AN: 4822

European-Finnish (FIN) AF: 0.435 AC: 4602 AN: 10568

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.383 AC: 26010 AN: 67980

Other (OTH) AF: 0.321 AC: 679 AN: 2114

Alfa AF: 0.359 Hom.: 17091

Bravo AF: 0.280

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.79
PhyloP100		-0.15
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: rs17477326; hg19: chr8-27603200;