rs1982040

chr18-69027979-A-G

Variant summary

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

The NM_024781.3(CCDC102B):c.1434+16875A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.824 in 152,096 control chromosomes in the GnomAD database, including 53,881 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 0.82 (53881 hom., cov: 32)
• Consequence: CCDC102B NM_024781.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.102

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 (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_024781.3	c.1434+16875A>G		intron_variant		ENST00000360242.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000360242.9	c.1434+16875A>G		intron_variant		1	NM_024781.3	P2

Frequencies

GnomAD3 genomes AF: 0.825 AC: 125373 AN: 151978 Hom.: 53899 Cov.: 32

Gnomad AFR AF: 0.578

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.845

Gnomad ASJ AF: 0.960

Gnomad EAS AF: 0.610

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.925

Gnomad MID AF: 0.877

Gnomad NFE AF: 0.955

Gnomad OTH AF: 0.850

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

GnomAD4 genome AF: 0.824 AC: 125377 AN: 152096 Hom.: 53881 Cov.: 32 AF XY: 0.824 AC XY: 61232 AN XY: 74350

Gnomad4 AFR AF: 0.577

Gnomad4 AMR AF: 0.844

Gnomad4 ASJ AF: 0.960

Gnomad4 EAS AF: 0.608

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.925

Gnomad4 NFE AF: 0.955

Gnomad4 OTH AF: 0.845

Alfa AF: 0.919 Hom.: 28221

Bravo AF: 0.804

Asia WGS AF: 0.712 AC: 2478 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	1.9
Dann	Benign	0.68

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: rs1982040; hg19: chr18-66695216;