18-68729625-T-C

Position:

• chr18-68729625-T-C

Variant summary

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

The NM_001093729.2(CCDC102B):​c.-48-5109T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.281 in 152,024 control chromosomes in the GnomAD database, including 7,493 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 0.28 (7493 hom., cov: 32)
• Consequence: CCDC102B NM_001093729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700

Genes affected

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

CCDC102B (HGNC:):

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 (EAS) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-48-5109T>C		intron_variant			NP_001087198.2
CCDC102B	XM_017025973.2	c.-48-5109T>C		intron_variant			XP_016881462.1
CCDC102B	XM_047437804.1	c.-99-5109T>C		intron_variant			XP_047293760.1
CCDC102B	XM_047437806.1	c.9+14269T>C		intron_variant			XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-48-5109T>C		intron_variant		1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-16+13031T>C		intron_variant		3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-67+13031T>C		intron_variant		4		ENSP00000461987.1
CCDC102B	ENST00000580292.2	n.117-5109T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.281 AC: 42681 AN: 151906 Hom.: 7496 Cov.: 32

Gnomad AFR AF: 0.0676

Gnomad AMI AF: 0.250

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.402

Gnomad SAS AF: 0.393

Gnomad FIN AF: 0.464

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.339

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.281 AC: 42671 AN: 152024 Hom.: 7493 Cov.: 32 AF XY: 0.292 AC XY: 21706 AN XY: 74298

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.383

Gnomad4 ASJ AF: 0.327

Gnomad4 EAS AF: 0.403

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.464

Gnomad4 NFE AF: 0.339

Gnomad4 OTH AF: 0.322

Alfa AF: 0.328 Hom.: 11785

Bravo AF: 0.264

Asia WGS AF: 0.358 AC: 1243 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	2.6
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2048329; hg19: chr18-66396862;