rs245311

chr5-127830907-A-Gchr5-127830907-A-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+32745A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.296 in 152,156 control chromosomes in the GnomAD database, including 6,787 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 0.30 (6787 hom., cov: 33)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.189

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 (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.411+32745A>G		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+32745A>G		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.468+32745A>G		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44968 AN: 152038 Hom.: 6789 Cov.: 33

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.411

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.284

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.296 AC: 44982 AN: 152156 Hom.: 6787 Cov.: 33 AF XY: 0.298 AC XY: 22181 AN XY: 74378

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.411

Gnomad4 SAS AF: 0.451

Gnomad4 FIN AF: 0.284

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.332

Alfa AF: 0.300 Hom.: 1195

Bravo AF: 0.298

Asia WGS AF: 0.435 AC: 1511 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	0.75
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs245311; hg19: chr5-127166599;