rs245199

Variant names:

• chr5-127841372-C-T
• rs245199
• NM_001317938.2:c.412-34166C>T

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-34166C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.744 in 152,110 control chromosomes in the GnomAD database, including 42,767 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 0.74 (42767 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.762
• Publications: 1 publications found

Genes affected

CCDC192 (HGNC:49566): (coiled-coil domain containing 192)

ENSG00000250603 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317938.2. 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
	CCDC192	NM_001317938.2	MANE Select	c.412-34166C>T		intron	N/A	NP_001304867.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.412-34166C>T		intron	N/A	ENSP00000490579.2
	CCDC192	ENST00000706942.1		c.469-34166C>T		intron	N/A	ENSP00000516662.1
	ENSG00000250603	ENST00000507509.1	TSL:2	n.192-2690G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.744 AC: 113086 AN: 151992 Hom.: 42711 Cov.: 32

Gnomad AFR AF: 0.882

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.704

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.744 AC: 113206 AN: 152110 Hom.: 42767 Cov.: 32 AF XY: 0.741 AC XY: 55046 AN XY: 74336

African (AFR) AF: 0.882 AC: 36628 AN: 41534

American (AMR) AF: 0.696 AC: 10619 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2310 AN: 3472

East Asian (EAS) AF: 0.591 AC: 3042 AN: 5150

South Asian (SAS) AF: 0.554 AC: 2675 AN: 4826

European-Finnish (FIN) AF: 0.717 AC: 7570 AN: 10556

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47897 AN: 67986

Other (OTH) AF: 0.713 AC: 1508 AN: 2114

Alfa AF: 0.731 Hom.: 12763

Bravo AF: 0.747

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.47
DANN	Benign	0.57
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs245199; hg19: chr5-127177064;