rs245199

Positions:

• chr5-127841372-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ENSG00000250603 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-34166C>T		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-34166C>T		intron_variant		5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-34166C>T		intron_variant				ENSP00000516662.1
ENSG00000250603	ENST00000507509.1	n.192-2690G>A		intron_variant		2

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

Gnomad4 AFR AF: 0.882

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.591

Gnomad4 SAS AF: 0.554

Gnomad4 FIN AF: 0.717

Gnomad4 NFE AF: 0.705

Gnomad4 OTH AF: 0.713

Alfa AF: 0.753 Hom.: 6195

Bravo AF: 0.747

Asia WGS AF: 0.578 AC: 2011 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245199; hg19: chr5-127177064;