19-17393187-C-T

Position:

• chr19-17393187-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC194	NM_001395222.1	c.324+648G>A		intron_variant		ENST00000636079.2	NP_001382151.1
CCDC194	NM_001395221.1	c.324+648G>A		intron_variant			NP_001382150.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC194	ENST00000636079.2	c.324+648G>A		intron_variant		5	NM_001395222.1	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

Gnomad4 AFR AF: 0.471

Gnomad4 AMR AF: 0.755

Gnomad4 ASJ AF: 0.871

Gnomad4 EAS AF: 0.429

Gnomad4 SAS AF: 0.712

Gnomad4 FIN AF: 0.791

Gnomad4 NFE AF: 0.885

Gnomad4 OTH AF: 0.753

Alfa AF: 0.854 Hom.: 72705

Bravo AF: 0.716

Asia WGS AF: 0.572 AC: 1992 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4808629; hg19: chr19-17503996;