rs1515641

Positions:

• chr5-127803924-G-A
• chr5-127803924-G-T

Variant summary

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

The NM_001317938.2(CCDC192):​c.411+5762G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0568 in 152,190 control chromosomes in the GnomAD database, including 558 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 0.057 (558 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.95

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=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.257 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.411+5762G>A		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+5762G>A		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.468+5762G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8645 AN: 152072 Hom.: 557 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.127

Gnomad ASJ AF: 0.0954

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0768

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.130

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0568 AC: 8652 AN: 152190 Hom.: 558 Cov.: 32 AF XY: 0.0595 AC XY: 4425 AN XY: 74424

Gnomad4 AFR AF: 0.0889

Gnomad4 AMR AF: 0.127

Gnomad4 ASJ AF: 0.0954

Gnomad4 EAS AF: 0.268

Gnomad4 SAS AF: 0.0770

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.0719

Alfa AF: 0.0285 Hom.: 227

Bravo AF: 0.0689

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.0030
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1515641; hg19: chr5-127139616;