rs6864687

Positions:

• chr5-127860374-G-A
• chr5-127860374-G-C

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-15164G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.392 in 151,852 control chromosomes in the GnomAD database, including 11,853 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 0.39 (11853 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83

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=-0.58).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.412-15164G>A		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-15164G>A		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.469-15164G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.392 AC: 59445 AN: 151734 Hom.: 11842 Cov.: 32

Gnomad AFR AF: 0.344

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.423

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.538

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.405

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.392 AC: 59478 AN: 151852 Hom.: 11853 Cov.: 32 AF XY: 0.392 AC XY: 29116 AN XY: 74192

Gnomad4 AFR AF: 0.344

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.375

Gnomad4 EAS AF: 0.538

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.405

Gnomad4 OTH AF: 0.390

Alfa AF: 0.399 Hom.: 25508

Bravo AF: 0.391

Asia WGS AF: 0.374 AC: 1301 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.58
CADD	Benign	13
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: rs6864687; hg19: chr5-127196066;