19-17393187-C-T

Variant names:

• chr19-17393187-C-T
• rs4808629
• NM_001395222.1:c.324+648G>A

Variant summary

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

The NM_001395222.1(CCDC194):​c.324+648G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.729 in 151,830 control chromosomes in the GnomAD database, including 42,930 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 (42930 hom., cov: 29)
• Consequence: CCDC194 NM_001395222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 7 publications found

Genes affected

CCDC194 (HGNC:53438): (coiled-coil domain containing 194)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.879 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395222.1. 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
	CCDC194	NM_001395222.1	MANE Select	c.324+648G>A		intron	N/A	NP_001382151.1
	CCDC194	NM_001395221.1		c.324+648G>A		intron	N/A	NP_001382150.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC194	ENST00000636079.2	TSL:5 MANE Select	c.324+648G>A		intron	N/A	ENSP00000490504.1

Frequencies

GnomAD3 genomes AF: 0.730 AC: 110714 AN: 151710 Hom.: 42938 Cov.: 29

Gnomad AFR AF: 0.471

Gnomad AMI AF: 0.874

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.871

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.791

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.885

Gnomad OTH AF: 0.758

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

GnomAD4 genome AF: 0.729 AC: 110731 AN: 151830 Hom.: 42930 Cov.: 29 AF XY: 0.722 AC XY: 53593 AN XY: 74206

African (AFR) AF: 0.471 AC: 19461 AN: 41328

American (AMR) AF: 0.755 AC: 11503 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.871 AC: 3024 AN: 3470

East Asian (EAS) AF: 0.429 AC: 2208 AN: 5146

South Asian (SAS) AF: 0.712 AC: 3434 AN: 4824

European-Finnish (FIN) AF: 0.791 AC: 8355 AN: 10558

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.885 AC: 60141 AN: 67964

Other (OTH) AF: 0.753 AC: 1582 AN: 2102

Alfa AF: 0.842 Hom.: 89894

Bravo AF: 0.716

Asia WGS AF: 0.572 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.4
DANN	Benign	0.71
PhyloP100		0.040

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4808629; hg19: chr19-17503996;