rs479017

Variant names:

• chr18-68758025-G-A
• rs479017
• ENST00000584775.5:c.-16+23259G>A

Variant summary

Our verdict is Benign. The variant received -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
• 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=-0.94).
• 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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 7 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-16+23259G>A		intron_variant	Intron 3 of 9		NP_001087198.2
CCDC102B	XM_017025973.2	c.-16+23259G>A		intron_variant	Intron 3 of 10		XP_016881462.1
CCDC102B	XM_047437804.1	c.-67+23259G>A		intron_variant	Intron 3 of 11		XP_047293760.1
CCDC102B	XM_047437806.1	c.9+42669G>A		intron_variant	Intron 1 of 7		XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-16+23259G>A		intron_variant	Intron 3 of 6	1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-16+41431G>A		intron_variant	Intron 2 of 2	3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-67+41431G>A		intron_variant	Intron 2 of 3	4		ENSP00000461987.1

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

African (AFR) AF: 0.0140 AC: 580 AN: 41512

American (AMR) AF: 0.00367 AC: 56 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3468

East Asian (EAS) AF: 0.0434 AC: 224 AN: 5166

South Asian (SAS) AF: 0.00334 AC: 16 AN: 4790

European-Finnish (FIN) AF: 0.0000946 AC: 1 AN: 10576

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000441 AC: 3 AN: 67954

Other (OTH) AF: 0.00475 AC: 10 AN: 2106

Alfa AF: 0.00316 Hom.: 1

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
PhyloP100		-0.23
Mutation Taster		=100/0	polymorphism

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: rs479017; hg19: chr18-66425262;