rs698171

chr5-127821068-A-Cchr5-127821068-A-T

Variant summary

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

The NM_001317938.2(CCDC192):c.411+22906A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,000 control chromosomes in the GnomAD database, including 10,061 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 0.35 (10061 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.267

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 (EAS) allele frequency at 95% confidence interval = 0.735 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.411+22906A>C		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+22906A>C		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.468+22906A>C		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53106 AN: 151882 Hom.: 10050 Cov.: 32

Gnomad AFR AF: 0.353

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.433

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.350 AC: 53146 AN: 152000 Hom.: 10061 Cov.: 32 AF XY: 0.353 AC XY: 26263 AN XY: 74298

Gnomad4 AFR AF: 0.353

Gnomad4 AMR AF: 0.434

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.755

Gnomad4 SAS AF: 0.508

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.297

Gnomad4 OTH AF: 0.368

Alfa AF: 0.312 Hom.: 6833

Bravo AF: 0.366

Asia WGS AF: 0.622 AC: 2159 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.5
Dann	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs698171; hg19: chr5-127156760;