rs698172

Positions:

• chr5-127819235-G-A
• chr5-127819235-G-C

Variant summary

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

The NM_001317938.2(CCDC192):​c.411+21073G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,966 control chromosomes in the GnomAD database, including 9,391 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 0.33 (9391 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.292

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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.411+21073G>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.411+21073G>A		intron_variant		5	NM_001317938.2	ENSP00000490579	A2
CCDC192	ENST00000706942.1	c.468+21073G>A		intron_variant				ENSP00000516662	P4

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50811 AN: 151848 Hom.: 9396 Cov.: 32

Gnomad AFR AF: 0.165

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.455

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.334 AC: 50813 AN: 151966 Hom.: 9391 Cov.: 32 AF XY: 0.335 AC XY: 24875 AN XY: 74274

Gnomad4 AFR AF: 0.165

Gnomad4 AMR AF: 0.381

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.403

Gnomad4 OTH AF: 0.365

Alfa AF: 0.382 Hom.: 6275

Bravo AF: 0.332

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.1
DANN	Benign	0.48

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs698172; hg19: chr5-127154927;