18-68715260-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001093729.2(CCDC102B):c.-217G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00317 in 1,328,876 control chromosomes in the GnomAD database, including 102 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.017 (62 hom., cov: 32)
  • Exomes 𝑓: 0.0014 (40 hom.)
• Consequence: CCDC102B NM_001093729.2 5_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.986

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BP6: Variant 18-68715260-G-A is Benign according to our data. Variant chr18-68715260-G-A is described in ClinVar as [Benign]. Clinvar id is 1260341.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0563 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_001093729.2	c.-217G>A		5_prime_UTR_variant	1/10
CCDC102B	XM_017025973.2	c.-217G>A		5_prime_UTR_variant	1/11
CCDC102B	XM_047437804.1	c.-268G>A		5_prime_UTR_variant	1/12
CCDC102B	XM_047437806.1	c.-88G>A		5_prime_UTR_variant	1/8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000578970.5	c.-235G>A		5_prime_UTR_variant	1/4	4
CCDC102B	ENST00000582077.5	n.52G>A		non_coding_transcript_exon_variant	1/3	2
CCDC102B	ENST00000584775.5			upstream_gene_variant		1
CCDC102B	ENST00000582371.5			upstream_gene_variant		3

Frequencies

GnomAD3 genomes AF: 0.0168 AC: 2559 AN: 152196 Hom.: 62 Cov.: 32

Gnomad AFR AF: 0.0583

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00681

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000206

Gnomad OTH AF: 0.0115

GnomAD4 exome AF: 0.00141 AC: 1654 AN: 1176562 Hom.: 40 Cov.: 29 AF XY: 0.00130 AC XY: 733 AN XY: 565964

Gnomad4 AFR exome AF: 0.0578

Gnomad4 AMR exome AF: 0.00379

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000236

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000731

Gnomad4 OTH exome AF: 0.00324

GnomAD4 genome AF: 0.0168 AC: 2562 AN: 152314 Hom.: 62 Cov.: 32 AF XY: 0.0161 AC XY: 1196 AN XY: 74472

Gnomad4 AFR AF: 0.0582

Gnomad4 AMR AF: 0.00680

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000207

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000206

Gnomad4 OTH AF: 0.0114

Alfa AF: 0.000788 Hom.: 0

Bravo AF: 0.0194

Asia WGS AF: 0.000577 AC: 2 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 25, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
Cadd	Benign	13
Dann	Benign	0.86

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: rs78924743; hg19: chr18-66382497;