rs10503122

Variant names:

• chr18-68782304-G-A
• rs10503122
• ENST00000584775.5:c.-16+47538G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-68782304-G-A
• chr18-68782304-G-C

Variant summary

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

The NM_001093729.2(CCDC102B):​c.-16+47538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0646 in 151,730 control chromosomes in the GnomAD database, including 592 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 0.065 (592 hom., cov: 32)
• Consequence: CCDC102B NM_001093729.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0740

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.153 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-16+47538G>A		intron_variant	Intron 3 of 9		NP_001087198.2
CCDC102B	XM_017025973.2	c.-16+47538G>A		intron_variant	Intron 3 of 10		XP_016881462.1
CCDC102B	XM_047437804.1	c.-66-41062G>A		intron_variant	Intron 3 of 11		XP_047293760.1
CCDC102B	XM_047437806.1	c.10-54445G>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+47538G>A		intron_variant	Intron 3 of 6	1		ENSP00000463538.1
CCDC102B	ENST00000582371.5	c.-15-54445G>A		intron_variant	Intron 2 of 2	3		ENSP00000463399.1
CCDC102B	ENST00000578970.5	c.-66-41062G>A		intron_variant	Intron 2 of 3	4		ENSP00000461987.1

Frequencies

GnomAD3 genomes AF: 0.0645 AC: 9775 AN: 151614 Hom.: 589 Cov.: 32

Gnomad AFR AF: 0.156

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0452

Gnomad ASJ AF: 0.0309

Gnomad EAS AF: 0.0566

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.0556

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0211

Gnomad OTH AF: 0.0596

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

GnomAD4 genome AF: 0.0646 AC: 9802 AN: 151730 Hom.: 592 Cov.: 32 AF XY: 0.0642 AC XY: 4760 AN XY: 74156

Gnomad4 AFR AF: 0.156

Gnomad4 AMR AF: 0.0451

Gnomad4 ASJ AF: 0.0309

Gnomad4 EAS AF: 0.0563

Gnomad4 SAS AF: 0.0220

Gnomad4 FIN AF: 0.0556

Gnomad4 NFE AF: 0.0210

Gnomad4 OTH AF: 0.0594

Alfa AF: 0.0186 Hom.: 12

Bravo AF: 0.0678

Asia WGS AF: 0.0630 AC: 218 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.0
DANN	Benign	0.34

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: rs10503122; hg19: chr18-66449541;