14-57488138-G-T

Variant names:

• chr14-57488138-G-T
• rs12147353
• NM_018168.4:c.306+2851C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC198	NM_018168.4	c.306+2851C>A		intron_variant	Intron 2 of 5	ENST00000216445.8	NP_060638.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC198	ENST00000216445.8	c.306+2851C>A		intron_variant	Intron 2 of 5	1	NM_018168.4	ENSP00000216445.3

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

African (AFR) AF: 0.193 AC: 7988 AN: 41494

American (AMR) AF: 0.445 AC: 6787 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3468

East Asian (EAS) AF: 0.807 AC: 4165 AN: 5164

South Asian (SAS) AF: 0.452 AC: 2182 AN: 4830

European-Finnish (FIN) AF: 0.610 AC: 6441 AN: 10560

Middle Eastern (MID) AF: 0.469 AC: 137 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41158 AN: 67956

Other (OTH) AF: 0.473 AC: 998 AN: 2108

Alfa AF: 0.538 Hom.: 25746

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
PhyloP100		0.16
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: rs12147353; hg19: chr14-57954856;