rs10463832

chr5-127774794-C-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317938.2(CCDC192):c.222+20419C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0556 in 152,198 control chromosomes in the GnomAD database, including 541 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 0.056 (541 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.975

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.222+20419C>A		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.222+20419C>A		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.279+20419C>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0555 AC: 8448 AN: 152082 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.0842

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0953

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0774

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0682

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

GnomAD4 genome AF: 0.0556 AC: 8455 AN: 152198 Hom.: 541 Cov.: 32 AF XY: 0.0584 AC XY: 4343 AN XY: 74408

Gnomad4 AFR AF: 0.0841

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0953

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0777

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.0713

Alfa AF: 0.0281 Hom.: 217

Bravo AF: 0.0676

Asia WGS AF: 0.177 AC: 615 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.58
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10463832; hg19: chr5-127110486;