rs12513840

Positions:

• chr5-127724250-A-G

Variant summary

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

The NM_001317938.2(CCDC192):​c.114+16490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0553 in 152,248 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 0.055 (541 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.258 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.114+16490A>G		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.114+16490A>G		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.171+16490A>G		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0553 AC: 8411 AN: 152130 Hom.: 540 Cov.: 32

Gnomad AFR AF: 0.0824

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0951

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.0832

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0553 AC: 8420 AN: 152248 Hom.: 541 Cov.: 32 AF XY: 0.0583 AC XY: 4343 AN XY: 74440

Gnomad4 AFR AF: 0.0823

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0951

Gnomad4 EAS AF: 0.270

Gnomad4 SAS AF: 0.0835

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0276 Hom.: 78

Bravo AF: 0.0676

Asia WGS AF: 0.168 AC: 583 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12513840; hg19: chr5-127059942;