18-68726003-C-T

Position:

• chr18-68726003-C-T

Variant summary

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

The ENST00000584775.5(CCDC102B):​c.-48-8731C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,118 control chromosomes in the GnomAD database, including 1,278 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 0.11 (1278 hom., cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-48-8731C>T		intron_variant			NP_001087198.2
CCDC102B	XM_017025973.2	c.-48-8731C>T		intron_variant			XP_016881462.1
CCDC102B	XM_047437804.1	c.-99-8731C>T		intron_variant			XP_047293760.1
CCDC102B	XM_047437806.1	c.9+10647C>T		intron_variant			XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-48-8731C>T		intron_variant		1		ENSP00000463538
CCDC102B	ENST00000578970.5	c.-67+9409C>T		intron_variant		4		ENSP00000461987
CCDC102B	ENST00000582371.5	c.-16+9409C>T		intron_variant		3		ENSP00000463399
CCDC102B	ENST00000580292.2	n.117-8731C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.111 AC: 16807 AN: 152000 Hom.: 1278 Cov.: 32

Gnomad AFR AF: 0.0419

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.112

Gnomad ASJ AF: 0.0923

Gnomad EAS AF: 0.370

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.0560

Gnomad MID AF: 0.175

Gnomad NFE AF: 0.129

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.111 AC: 16809 AN: 152118 Hom.: 1278 Cov.: 32 AF XY: 0.112 AC XY: 8324 AN XY: 74364

Gnomad4 AFR AF: 0.0419

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0923

Gnomad4 EAS AF: 0.370

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.0560

Gnomad4 NFE AF: 0.129

Gnomad4 OTH AF: 0.113

Alfa AF: 0.123 Hom.: 1733

Bravo AF: 0.108

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
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: rs17079623; hg19: chr18-66393240;