rs8092610

Variant names:

• chr18-68794653-C-T
• rs8092610
• ENST00000584775.5:c.-15-42096C>T

Variant summary

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

The ENST00000584775.5(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 ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.780
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-15-42096C>T		intron_variant	Intron 3 of 9		NP_001087198.2
CCDC102B	XM_017025973.2	c.-15-42096C>T		intron_variant	Intron 3 of 10		XP_016881462.1
CCDC102B	XM_047437804.1	c.-66-28713C>T		intron_variant	Intron 3 of 11		XP_047293760.1
CCDC102B	XM_047437806.1	c.10-42096C>T		intron_variant	Intron 1 of 7		XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-15-42096C>T		intron_variant	Intron 3 of 6	1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-15-42096C>T		intron_variant	Intron 2 of 2	3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-66-28713C>T		intron_variant	Intron 2 of 3	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

African (AFR) AF: 0.175 AC: 7272 AN: 41468

American (AMR) AF: 0.0450 AC: 686 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.0429 AC: 149 AN: 3472

East Asian (EAS) AF: 0.0546 AC: 283 AN: 5180

South Asian (SAS) AF: 0.0211 AC: 102 AN: 4828

European-Finnish (FIN) AF: 0.0559 AC: 591 AN: 10568

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0211 AC: 1435 AN: 67980

Other (OTH) AF: 0.0668 AC: 141 AN: 2112

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
PhyloP100		0.78
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: rs8092610; hg19: chr18-66461890;