rs17477326

chr8-27745683-G-Achr8-27745683-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC25	NM_018246.3	c.551+2394C>T		intron_variant		ENST00000356537.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC25	ENST00000356537.9	c.551+2394C>T		intron_variant		1	NM_018246.3	P1
	ENST00000521510.2	n.648-7238G>A		intron_variant, non_coding_transcript_variant		4

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

Gnomad4 AFR AF: 0.124

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.480

Gnomad4 EAS AF: 0.120

Gnomad4 SAS AF: 0.349

Gnomad4 FIN AF: 0.435

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.321

Alfa AF: 0.368 Hom.: 14094

Bravo AF: 0.280

Asia WGS AF: 0.220 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	1.2
Dann	Benign	0.79

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: rs17477326; hg19: chr8-27603200;