14-57488138-G-T

Variant summary

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

The NM_018168.4(CCDC198):c.306+2851C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.474 in 152,050 control chromosomes in the GnomAD database, including 19,685 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 0.47 (19685 hom., cov: 32)
• Consequence: CCDC198 NM_018168.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.157

Genes affected

CCDC198 (HGNC:20189): (coiled-coil domain containing 198)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.786 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC198	NM_018168.4	c.306+2851C>A		intron_variant		ENST00000216445.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC198	ENST00000216445.8	c.306+2851C>A		intron_variant		1	NM_018168.4	A1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 72091 AN: 151932 Hom.: 19696 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.444

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.806

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.479

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

GnomAD4 genome AF: 0.474 AC: 72075 AN: 152050 Hom.: 19685 Cov.: 32 AF XY: 0.475 AC XY: 35323 AN XY: 74334

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.445

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.606

Gnomad4 OTH AF: 0.473

Alfa AF: 0.556 Hom.: 21025

Bravo AF: 0.449

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	8.6
Dann	Benign	0.66

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: rs12147353; hg19: chr14-57954856;