rs17240415

Positions:

• chr18-68983651-G-T

Variant summary

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

The NM_024781.3(CCDC102B):​c.1264-27283G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 151,610 control chromosomes in the GnomAD database, including 4,951 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 0.24 (4951 hom., cov: 32)
• Consequence: CCDC102B NM_024781.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.440

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=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC102B	NM_024781.3	c.1264-27283G>T		intron_variant		ENST00000360242.9	NP_079057.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000360242.9	c.1264-27283G>T		intron_variant		1	NM_024781.3	ENSP00000353377.5
CCDC102B	ENST00000584156.5	c.1264-27283G>T		intron_variant		1		ENSP00000463111.1

Frequencies

GnomAD3 genomes AF: 0.237 AC: 35847 AN: 151492 Hom.: 4959 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.298

Gnomad OTH AF: 0.275

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

GnomAD4 genome AF: 0.236 AC: 35825 AN: 151610 Hom.: 4951 Cov.: 32 AF XY: 0.235 AC XY: 17413 AN XY: 74074

Gnomad4 AFR AF: 0.101

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.474

Gnomad4 EAS AF: 0.202

Gnomad4 SAS AF: 0.345

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.271

Alfa AF: 0.301 Hom.: 9186

Bravo AF: 0.233

Asia WGS AF: 0.261 AC: 905 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.46

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

Publications

LitVar

Other links and lift over

dbSNP: rs17240415; hg19: chr18-66650888;