rs181746

chr5-127856969-G-A

Variant summary

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

The NM_001317938.2(CCDC192):c.412-18569G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,124 control chromosomes in the GnomAD database, including 37,609 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 0.70 (37609 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.539

Genes affected

CCDC192 (HGNC:49566): (coiled-coil domain containing 192)

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.756 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.412-18569G>A		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-18569G>A		intron_variant		5	NM_001317938.2	A2
	ENST00000507509.1	n.191+645C>T		intron_variant, non_coding_transcript_variant		2
CCDC192	ENST00000706942.1	c.469-18569G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106674 AN: 152006 Hom.: 37562 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.668

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.546

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.694

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.702 AC: 106782 AN: 152124 Hom.: 37609 Cov.: 32 AF XY: 0.700 AC XY: 52021 AN XY: 74342

Gnomad4 AFR AF: 0.763

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.547

Gnomad4 FIN AF: 0.716

Gnomad4 NFE AF: 0.694

Gnomad4 OTH AF: 0.670

Alfa AF: 0.707 Hom.: 4744

Bravo AF: 0.699

Asia WGS AF: 0.563 AC: 1960 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.64
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181746; hg19: chr5-127192661;