rs479017

chr18-68758025-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000584775.5(CCDC102B):c.-16+23259G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00586 in 152,026 control chromosomes in the GnomAD database, including 7 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 0.0059 (7 hom., cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.230

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=-0.94).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.00586 (891/152026) while in subpopulation EAS AF= 0.0434 (224/5166). AF 95% confidence interval is 0.0387. There are 7 homozygotes in gnomad4. There are 453 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_001093729.2	c.-16+23259G>A		intron_variant
CCDC102B	XM_017025973.2	c.-16+23259G>A		intron_variant
CCDC102B	XM_047437804.1	c.-67+23259G>A		intron_variant
CCDC102B	XM_047437806.1	c.9+42669G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-16+23259G>A		intron_variant		1
CCDC102B	ENST00000578970.5	c.-67+41431G>A		intron_variant		4
CCDC102B	ENST00000582371.5	c.-16+41431G>A		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.00585 AC: 889 AN: 151908 Hom.: 7 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00374

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.0433

Gnomad SAS AF: 0.00334

Gnomad FIN AF: 0.0000946

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00480

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

GnomAD4 genome AF: 0.00586 AC: 891 AN: 152026 Hom.: 7 Cov.: 32 AF XY: 0.00610 AC XY: 453 AN XY: 74278

Gnomad4 AFR AF: 0.0140

Gnomad4 AMR AF: 0.00367

Gnomad4 ASJ AF: 0.000288

Gnomad4 EAS AF: 0.0434

Gnomad4 SAS AF: 0.00334

Gnomad4 FIN AF: 0.0000946

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00475

Alfa AF: 0.00374 Hom.: 0

Bravo AF: 0.00754

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.91
Dann	Benign	0.60

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: rs479017; hg19: chr18-66425262;