5-127871843-G-A

Position:

• chr5-127871843-G-A

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-3695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,050 control chromosomes in the GnomAD database, including 33,502 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 0.66 (33502 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142

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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-3695G>A		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-3695G>A		intron_variant		5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-3695G>A		intron_variant				ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100705 AN: 151932 Hom.: 33477 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.663 AC: 100778 AN: 152050 Hom.: 33502 Cov.: 32 AF XY: 0.661 AC XY: 49084 AN XY: 74300

Gnomad4 AFR AF: 0.626

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.588

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.697

Gnomad4 OTH AF: 0.644

Alfa AF: 0.685 Hom.: 13833

Bravo AF: 0.656

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245183; hg19: chr5-127207535;