rs1539893

Variant names:

• chr18-68877518-G-A
• rs1539893
• NM_024781.3:c.1053+2733G>A

Your query was ambiguous. Multiple possible variants found:

• chr18-68877518-G-A
• chr18-68877518-G-C
• chr18-68877518-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC102B	NM_024781.3	c.1053+2733G>A		intron_variant	Intron 5 of 7	ENST00000360242.9	NP_079057.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC102B	ENST00000360242.9	c.1053+2733G>A		intron_variant	Intron 5 of 7	1	NM_024781.3	ENSP00000353377.5
CCDC102B	ENST00000584156.5	c.1053+2733G>A		intron_variant	Intron 4 of 5	1		ENSP00000463111.1
CCDC102B	ENST00000577772.5	n.1111+2733G>A		intron_variant	Intron 5 of 6	2
CCDC102B	ENST00000577800.1	n.175+2733G>A		intron_variant	Intron 2 of 2	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

African (AFR) AF: 0.491 AC: 20340 AN: 41434

American (AMR) AF: 0.766 AC: 11703 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.849 AC: 2949 AN: 3472

East Asian (EAS) AF: 0.792 AC: 4097 AN: 5176

South Asian (SAS) AF: 0.804 AC: 3882 AN: 4828

European-Finnish (FIN) AF: 0.853 AC: 9029 AN: 10590

Middle Eastern (MID) AF: 0.867 AC: 255 AN: 294

European-Non Finnish (NFE) AF: 0.830 AC: 56423 AN: 67982

Other (OTH) AF: 0.765 AC: 1615 AN: 2110

Alfa AF: 0.800 Hom.: 93803

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
PhyloP100		-0.29
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1539893; hg19: chr18-66544755;