rs309244

Variant names:

• chr18-68717124-G-A
• rs309244
• ENST00000584775.5:c.-49+530G>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.-49+530G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00696 in 152,068 control chromosomes in the GnomAD database, including 10 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 0.0070 (10 hom., cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.593
• 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=-0.98).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.00696 (1058/152068) while in subpopulation AFR AF = 0.0234 (972/41452). AF 95% confidence interval is 0.0222. There are 10 homozygotes in GnomAd4. There are 486 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 10 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-49+530G>A		intron_variant	Intron 2 of 9		NP_001087198.2
CCDC102B	XM_017025973.2	c.-49+530G>A		intron_variant	Intron 2 of 10		XP_016881462.1
CCDC102B	XM_047437804.1	c.-100+530G>A		intron_variant	Intron 2 of 11		XP_047293760.1
CCDC102B	XM_047437806.1	c.9+1768G>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.-49+530G>A		intron_variant	Intron 2 of 6	1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-16+530G>A		intron_variant	Intron 2 of 2	3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-67+530G>A		intron_variant	Intron 2 of 3	4		ENSP00000461987.1

Frequencies

GnomAD3 genomes AF: 0.00694 AC: 1055 AN: 151952 Hom.: 10 Cov.: 32

Gnomad AFR AF: 0.0234

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00413

Gnomad ASJ AF: 0.000288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000208

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000147

Gnomad OTH AF: 0.00526

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

GnomAD4 genome AF: 0.00696 AC: 1058 AN: 152068 Hom.: 10 Cov.: 32 AF XY: 0.00654 AC XY: 486 AN XY: 74352

African (AFR) AF: 0.0234 AC: 972 AN: 41452

American (AMR) AF: 0.00412 AC: 63 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.000288 AC: 1 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5182

South Asian (SAS) AF: 0.000208 AC: 1 AN: 4800

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10580

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

European-Non Finnish (NFE) AF: 0.000147 AC: 10 AN: 67990

Other (OTH) AF: 0.00521 AC: 11 AN: 2112

Alfa AF: 0.00651 Hom.: 1

Bravo AF: 0.00764

Asia WGS AF: 0.00173 AC: 6 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	5.2
DANN	Benign	0.45
PhyloP100		0.59

Splicing

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

Other links and lift over

dbSNP: rs309244; hg19: chr18-66384361;