NM_001378204.1:c.3199-3054G>T

Variant names:

• chr1-93251417-G-T
• rs797680
• NM_001378204.1:c.3199-3054G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001378204.1(CCDC18):​c.3199-3054G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.505 in 151,986 control chromosomes in the GnomAD database, including 22,963 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 0.50 (22963 hom., cov: 32)
• Consequence: CCDC18 NM_001378204.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710
• Publications: 7 publications found

Genes affected

CCDC18 (HGNC:30370): (coiled-coil domain containing 18)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.838 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001378204.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC18	NM_001378204.1	MANE Select	c.3199-3054G>T		intron	N/A	NP_001365133.1
	CCDC18	NM_001306076.1		c.3196-3054G>T		intron	N/A	NP_001293005.1
	CCDC18	NM_206886.4		c.3199-3054G>T		intron	N/A	NP_996769.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC18	ENST00000690025.1	MANE Select	c.3199-3054G>T		intron	N/A	ENSP00000510597.1
	CCDC18	ENST00000401026.7	TSL:1	c.3199-3054G>T		intron	N/A	ENSP00000383808.3
	CCDC18	ENST00000343253.11	TSL:5	c.3196-3054G>T		intron	N/A	ENSP00000343377.7

Frequencies

GnomAD3 genomes AF: 0.504 AC: 76562 AN: 151868 Hom.: 22899 Cov.: 32

Gnomad AFR AF: 0.845

Gnomad AMI AF: 0.369

Gnomad AMR AF: 0.445

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.371

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.505 AC: 76695 AN: 151986 Hom.: 22963 Cov.: 32 AF XY: 0.500 AC XY: 37158 AN XY: 74292

African (AFR) AF: 0.846 AC: 35096 AN: 41492

American (AMR) AF: 0.445 AC: 6798 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1175 AN: 3458

East Asian (EAS) AF: 0.349 AC: 1805 AN: 5174

South Asian (SAS) AF: 0.322 AC: 1549 AN: 4818

European-Finnish (FIN) AF: 0.347 AC: 3660 AN: 10538

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.371 AC: 25213 AN: 67922

Other (OTH) AF: 0.454 AC: 958 AN: 2110

Alfa AF: 0.378 Hom.: 10253

Bravo AF: 0.531

Asia WGS AF: 0.396 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.16
PhyloP100		-0.71
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: rs797680; hg19: chr1-93716974;