rs8092610

Positions:

• chr18-68794653-C-T

Variant summary

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

The NM_001093729.2(CCDC102B):​c.-15-42096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,048 control chromosomes in the GnomAD database, including 723 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 0.070 (723 hom., cov: 31)
• Consequence: CCDC102B NM_001093729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780

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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.172 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-15-42096C>T		intron_variant			NP_001087198.2
CCDC102B	XM_017025973.2	c.-15-42096C>T		intron_variant			XP_016881462.1
CCDC102B	XM_047437804.1	c.-66-28713C>T		intron_variant			XP_047293760.1
CCDC102B	XM_047437806.1	c.10-42096C>T		intron_variant			XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-15-42096C>T		intron_variant		1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-15-42096C>T		intron_variant		3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-66-28713C>T		intron_variant		4		ENSP00000461987.1

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10658 AN: 151930 Hom.: 721 Cov.: 31

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0451

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.0549

Gnomad SAS AF: 0.0215

Gnomad FIN AF: 0.0559

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0670

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

GnomAD4 genome AF: 0.0702 AC: 10677 AN: 152048 Hom.: 723 Cov.: 31 AF XY: 0.0698 AC XY: 5190 AN XY: 74344

Gnomad4 AFR AF: 0.175

Gnomad4 AMR AF: 0.0450

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.0546

Gnomad4 SAS AF: 0.0211

Gnomad4 FIN AF: 0.0559

Gnomad4 NFE AF: 0.0211

Gnomad4 OTH AF: 0.0668

Alfa AF: 0.0520 Hom.: 51

Bravo AF: 0.0747

Asia WGS AF: 0.0590 AC: 204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.5
DANN	Benign	0.54

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: rs8092610; hg19: chr18-66461890;