ENST00000584775.5:c.-16+47367A>G

Variant names:

• chr18-68782133-A-G
• rs1676853
• ENST00000584775.5:c.-16+47367A>G

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.99).
• 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 rank	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-16+47367A>G		intron_variant	Intron 3 of 9		NP_001087198.2
CCDC102B	XM_017025973.2	c.-16+47367A>G		intron_variant	Intron 3 of 10		XP_016881462.1
CCDC102B	XM_047437804.1	c.-66-41233A>G		intron_variant	Intron 3 of 11		XP_047293760.1
CCDC102B	XM_047437806.1	c.10-54616A>G		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.-16+47367A>G		intron_variant	Intron 3 of 6	1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-15-54616A>G		intron_variant	Intron 2 of 2	3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-66-41233A>G		intron_variant	Intron 2 of 3	4		ENSP00000461987.1

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

African (AFR) AF: 0.177 AC: 7344 AN: 41468

American (AMR) AF: 0.0500 AC: 765 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0311 AC: 108 AN: 3472

East Asian (EAS) AF: 0.0993 AC: 514 AN: 5178

South Asian (SAS) AF: 0.0244 AC: 118 AN: 4830

European-Finnish (FIN) AF: 0.0554 AC: 586 AN: 10586

Middle Eastern (MID) AF: 0.0582 AC: 17 AN: 292

European-Non Finnish (NFE) AF: 0.0211 AC: 1433 AN: 67976

Other (OTH) AF: 0.0649 AC: 137 AN: 2110

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
PhyloP100		-0.12
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: rs1676853; hg19: chr18-66449370;