rs7722425

Positions:

• chr5-127790070-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.223-7033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,214 control chromosomes in the GnomAD database, including 3,591 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 0.14 (3591 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.214

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=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.223-7033T>C		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.223-7033T>C		intron_variant		5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.280-7033T>C		intron_variant				ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21656 AN: 152096 Hom.: 3582 Cov.: 33

Gnomad AFR AF: 0.386

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.0961

Gnomad EAS AF: 0.268

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0120

Gnomad OTH AF: 0.127

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

GnomAD4 genome AF: 0.143 AC: 21705 AN: 152214 Hom.: 3591 Cov.: 33 AF XY: 0.142 AC XY: 10565 AN XY: 74450

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.159

Gnomad4 ASJ AF: 0.0961

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0782

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0120

Gnomad4 OTH AF: 0.129

Alfa AF: 0.0740 Hom.: 523

Bravo AF: 0.168

Asia WGS AF: 0.197 AC: 686 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.5
DANN	Benign	0.88

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7722425; hg19: chr5-127125762;