rs1676853

chr18-68782133-A-G

Variant summary

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

The ENST00000584775.5(CCDC102B):c.-16+47367A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0725 in 152,110 control chromosomes in the GnomAD database, including 760 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 0.072 (760 hom., cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.117

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_001093729.2	c.-16+47367A>G		intron_variant
CCDC102B	XM_017025973.2	c.-16+47367A>G		intron_variant
CCDC102B	XM_047437804.1	c.-66-41233A>G		intron_variant
CCDC102B	XM_047437806.1	c.10-54616A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-16+47367A>G		intron_variant		1
CCDC102B	ENST00000578970.5	c.-66-41233A>G		intron_variant		4
CCDC102B	ENST00000582371.5	c.-15-54616A>G		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0723 AC: 10993 AN: 151990 Hom.: 756 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0502

Gnomad ASJ AF: 0.0311

Gnomad EAS AF: 0.0994

Gnomad SAS AF: 0.0248

Gnomad FIN AF: 0.0554

Gnomad MID AF: 0.0545

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0651

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

GnomAD4 genome AF: 0.0725 AC: 11022 AN: 152110 Hom.: 760 Cov.: 32 AF XY: 0.0721 AC XY: 5365 AN XY: 74382

Gnomad4 AFR AF: 0.177

Gnomad4 AMR AF: 0.0500

Gnomad4 ASJ AF: 0.0311

Gnomad4 EAS AF: 0.0993

Gnomad4 SAS AF: 0.0244

Gnomad4 FIN AF: 0.0554

Gnomad4 NFE AF: 0.0211

Gnomad4 OTH AF: 0.0649

Alfa AF: 0.0517 Hom.: 54

Bravo AF: 0.0778

Asia WGS AF: 0.0770 AC: 263 AN: 3444

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	2.6
Dann	Benign	0.56

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: rs1676853; hg19: chr18-66449370;