chr1-93251417-G-T

Position:

• chr1-93251417-G-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC18	NM_001378204.1	c.3199-3054G>T		intron_variant		ENST00000690025.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC18	ENST00000690025.1	c.3199-3054G>T		intron_variant			NM_001378204.1	P4

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

Gnomad4 AFR AF: 0.846

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.340

Gnomad4 EAS AF: 0.349

Gnomad4 SAS AF: 0.322

Gnomad4 FIN AF: 0.347

Gnomad4 NFE AF: 0.371

Gnomad4 OTH AF: 0.454

Alfa AF: 0.368 Hom.: 8485

Bravo AF: 0.531

Asia WGS AF: 0.396 AC: 1376 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.78
DANN	Benign	0.16

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: rs797680; hg19: chr1-93716974;