18-68726003-C-T

Variant names:

• chr18-68726003-C-T
• rs17079623
• ENST00000584775.5:c.-48-8731C>T

Variant summary

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

The NM_001093729.2(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 NM_001093729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74
• Publications: 6 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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001093729.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC102B	NM_001093729.2		c.-48-8731C>T		intron	N/A	NP_001087198.2	Q68D86-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC102B	ENST00000584775.5	TSL:1	c.-48-8731C>T		intron	N/A	ENSP00000463538.1	J3QLG6
	CCDC102B	ENST00000903417.1		c.-16+9409C>T		intron	N/A	ENSP00000573476.1
	CCDC102B	ENST00000903418.1		c.-48-8731C>T		intron	N/A	ENSP00000573477.1

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

African (AFR) AF: 0.0419 AC: 1738 AN: 41496

American (AMR) AF: 0.112 AC: 1711 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0923 AC: 320 AN: 3468

East Asian (EAS) AF: 0.370 AC: 1909 AN: 5158

South Asian (SAS) AF: 0.254 AC: 1226 AN: 4824

European-Finnish (FIN) AF: 0.0560 AC: 593 AN: 10586

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.129 AC: 8796 AN: 67994

Other (OTH) AF: 0.113 AC: 238 AN: 2114

Alfa AF: 0.116 Hom.: 2284

Bravo AF: 0.108

Asia WGS AF: 0.268 AC: 930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	10
DANN	Benign	0.75
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs17079623; hg19: chr18-66393240;