rs17079623

Positions:

• chr18-68726003-C-A
• chr18-68726003-C-T

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000584775.5(CCDC102B):​c.-48-8731C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
• Consequence: CCDC102B ENST00000584775.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.74

Genes affected

CCDC102B (HGNC:26295): (coiled-coil domain containing 102B)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC102B	NM_001093729.2	c.-48-8731C>A		intron_variant			NP_001087198.2
CCDC102B	XM_017025973.2	c.-48-8731C>A		intron_variant			XP_016881462.1
CCDC102B	XM_047437804.1	c.-99-8731C>A		intron_variant			XP_047293760.1
CCDC102B	XM_047437806.1	c.9+10647C>A		intron_variant			XP_047293762.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000584775.5	c.-48-8731C>A		intron_variant		1		ENSP00000463538
CCDC102B	ENST00000578970.5	c.-67+9409C>A		intron_variant		4		ENSP00000461987
CCDC102B	ENST00000582371.5	c.-16+9409C>A		intron_variant		3		ENSP00000463399
CCDC102B	ENST00000580292.2	n.117-8731C>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	8.0
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17079623; hg19: chr18-66393240;