rs12523164

chr5-127726279-T-C

Variant summary

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

The NM_001317938.2(CCDC192):c.114+18519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0558 in 152,306 control chromosomes in the GnomAD database, including 553 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 0.056 (553 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.114+18519T>C		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.114+18519T>C		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.171+18519T>C		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8483 AN: 152188 Hom.: 552 Cov.: 33

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0956

Gnomad EAS AF: 0.271

Gnomad SAS AF: 0.0862

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0698

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

GnomAD4 genome AF: 0.0558 AC: 8493 AN: 152306 Hom.: 553 Cov.: 33 AF XY: 0.0588 AC XY: 4379 AN XY: 74466

Gnomad4 AFR AF: 0.0830

Gnomad4 AMR AF: 0.128

Gnomad4 ASJ AF: 0.0956

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.0864

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.0728

Alfa AF: 0.0316 Hom.: 31

Bravo AF: 0.0677

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	4.5
Dann	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12523164; hg19: chr5-127061971;