chr5-127869728-C-T

Position:

• chr5-127869728-C-T

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-5810C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,168 control chromosomes in the GnomAD database, including 42,206 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 0.74 (42206 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.265

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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.871 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-5810C>T		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-5810C>T		intron_variant		5	NM_001317938.2	ENSP00000490579	A2
CCDC192	ENST00000706942.1	c.469-5810C>T		intron_variant				ENSP00000516662	P4

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112351 AN: 152050 Hom.: 42154 Cov.: 33

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.694

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.589

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.739 AC: 112465 AN: 152168 Hom.: 42206 Cov.: 33 AF XY: 0.735 AC XY: 54661 AN XY: 74370

Gnomad4 AFR AF: 0.878

Gnomad4 AMR AF: 0.694

Gnomad4 ASJ AF: 0.665

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.550

Gnomad4 FIN AF: 0.699

Gnomad4 NFE AF: 0.699

Gnomad4 OTH AF: 0.713

Alfa AF: 0.730 Hom.: 5078

Bravo AF: 0.743

Asia WGS AF: 0.575 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.78
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245181; hg19: chr5-127205420;