rs17240415

Variant names:

• chr18-68983651-G-T
• rs17240415
• NM_024781.3:c.1264-27283G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.92).
• 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 rank	MANE	Protein	UniProt
CCDC102B	NM_024781.3	c.1264-27283G>T		intron_variant	Intron 6 of 7	ENST00000360242.9	NP_079057.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000360242.9	c.1264-27283G>T		intron_variant	Intron 6 of 7	1	NM_024781.3	ENSP00000353377.5
CCDC102B	ENST00000584156.5	c.1264-27283G>T		intron_variant	Intron 5 of 5	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

African (AFR) AF: 0.101 AC: 4163 AN: 41390

American (AMR) AF: 0.268 AC: 4070 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1642 AN: 3462

East Asian (EAS) AF: 0.202 AC: 1039 AN: 5144

South Asian (SAS) AF: 0.345 AC: 1664 AN: 4828

European-Finnish (FIN) AF: 0.194 AC: 2042 AN: 10508

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.298 AC: 20217 AN: 67780

Other (OTH) AF: 0.271 AC: 572 AN: 2108

Alfa AF: 0.287 Hom.: 17900

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
PhyloP100		-0.44
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs17240415; hg19: chr18-66650888;