rs1539893

chr18-68877518-G-Achr18-68877518-G-Cchr18-68877518-G-T

Variant summary

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

The NM_024781.3(CCDC102B):c.1053+2733G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,086 control chromosomes in the GnomAD database, including 42,187 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 0.73 (42187 hom., cov: 32)
• Consequence: CCDC102B NM_024781.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.288

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=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.824 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC102B	NM_024781.3	c.1053+2733G>A		intron_variant		ENST00000360242.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC102B	ENST00000360242.9	c.1053+2733G>A		intron_variant		1	NM_024781.3	P2
CCDC102B	ENST00000584156.5	c.1053+2733G>A		intron_variant		1		A2
CCDC102B	ENST00000577772.5	n.1111+2733G>A		intron_variant, non_coding_transcript_variant		2
CCDC102B	ENST00000577800.1	n.175+2733G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.730 AC: 111007 AN: 151968 Hom.: 42182 Cov.: 32

Gnomad AFR AF: 0.491

Gnomad AMI AF: 0.818

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.849

Gnomad EAS AF: 0.791

Gnomad SAS AF: 0.803

Gnomad FIN AF: 0.853

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.830

Gnomad OTH AF: 0.770

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

GnomAD4 genome AF: 0.730 AC: 111039 AN: 152086 Hom.: 42187 Cov.: 32 AF XY: 0.736 AC XY: 54715 AN XY: 74386

Gnomad4 AFR AF: 0.491

Gnomad4 AMR AF: 0.766

Gnomad4 ASJ AF: 0.849

Gnomad4 EAS AF: 0.792

Gnomad4 SAS AF: 0.804

Gnomad4 FIN AF: 0.853

Gnomad4 NFE AF: 0.830

Gnomad4 OTH AF: 0.765

Alfa AF: 0.813 Hom.: 69880

Bravo AF: 0.714

Asia WGS AF: 0.743 AC: 2585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.21
Dann	Benign	0.63

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: rs1539893; hg19: chr18-66544755;