18-68729625-T-C

Variant names:

• chr18-68729625-T-C
• rs2048329
• ENST00000584775.5:c.-48-5109T>C

Variant summary

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

The NM_001093729.2(CCDC102B):​c.-48-5109T>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
• Publications: 3 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.388 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.-48-5109T>C		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.-48-5109T>C		intron	N/A	ENSP00000463538.1	J3QLG6
	CCDC102B	ENST00000903417.1		c.-16+13031T>C		intron	N/A	ENSP00000573476.1
	CCDC102B	ENST00000903418.1		c.-48-5109T>C		intron	N/A	ENSP00000573477.1

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

African (AFR) AF: 0.0674 AC: 2798 AN: 41492

American (AMR) AF: 0.383 AC: 5855 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1135 AN: 3466

East Asian (EAS) AF: 0.403 AC: 2077 AN: 5160

South Asian (SAS) AF: 0.392 AC: 1888 AN: 4822

European-Finnish (FIN) AF: 0.464 AC: 4893 AN: 10556

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.339 AC: 23048 AN: 67932

Other (OTH) AF: 0.322 AC: 679 AN: 2108

Alfa AF: 0.321 Hom.: 15716

Bravo AF: 0.264

Asia WGS AF: 0.358 AC: 1243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.6
DANN	Benign	0.75
PhyloP100		0.070

Splicing

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

Other links and lift over

dbSNP: rs2048329; hg19: chr18-66396862;