rs309247

chr18-68715827-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000584775.5(CCDC102B):c.-116+466C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0691 in 152,126 control chromosomes in the GnomAD database, including 1,134 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 0.069 (1134 hom., cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

CCDC102B (HGNC:26295): (coiled-coil domain containing 102B)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.225 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_001093729.2	c.-116+466C>G		intron_variant
CCDC102B	XM_017025973.2	c.-116+466C>G		intron_variant
CCDC102B	XM_047437804.1	c.-167+466C>G		intron_variant
CCDC102B	XM_047437806.1	c.9+471C>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-116+466C>G		intron_variant		1
CCDC102B	ENST00000578970.5	c.-134+466C>G		intron_variant		4
CCDC102B	ENST00000582371.5	c.-83+466C>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0690 AC: 10496 AN: 152008 Hom.: 1126 Cov.: 32

Gnomad AFR AF: 0.229

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0412

Gnomad ASJ AF: 0.00749

Gnomad EAS AF: 0.0156

Gnomad SAS AF: 0.00249

Gnomad FIN AF: 0.000283

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00193

Gnomad OTH AF: 0.0617

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

GnomAD4 genome AF: 0.0691 AC: 10517 AN: 152126 Hom.: 1134 Cov.: 32 AF XY: 0.0672 AC XY: 4996 AN XY: 74364

Gnomad4 AFR AF: 0.229

Gnomad4 AMR AF: 0.0410

Gnomad4 ASJ AF: 0.00749

Gnomad4 EAS AF: 0.0156

Gnomad4 SAS AF: 0.00250

Gnomad4 FIN AF: 0.000283

Gnomad4 NFE AF: 0.00193

Gnomad4 OTH AF: 0.0629

Alfa AF: 0.0411 Hom.: 78

Bravo AF: 0.0794

Asia WGS AF: 0.0310 AC: 109 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.64
Dann	Benign	0.35

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs309247; hg19: chr18-66383064;