rs248742

Positions:

• chr5-127710314-C-G
• chr5-127710314-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.114+2554C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,760 control chromosomes in the GnomAD database, including 7,614 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 0.31 (7614 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.994

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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.413 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.114+2554C>G		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.114+2554C>G		intron_variant		5	NM_001317938.2	ENSP00000490579	A2
CCDC192	ENST00000706942.1	c.171+2554C>G		intron_variant				ENSP00000516662	P4

Frequencies

GnomAD3 genomes AF: 0.310 AC: 46975 AN: 151642 Hom.: 7610 Cov.: 31

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.323

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.377

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.330

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.333

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.310 AC: 46985 AN: 151760 Hom.: 7614 Cov.: 31 AF XY: 0.313 AC XY: 23240 AN XY: 74166

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.374

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.428

Gnomad4 FIN AF: 0.330

Gnomad4 NFE AF: 0.333

Gnomad4 OTH AF: 0.324

Alfa AF: 0.184 Hom.: 402

Bravo AF: 0.310

Asia WGS AF: 0.392 AC: 1362 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.42
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248742; hg19: chr5-127046006;