Variant rs10463833 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001317938.2(CCDC192):c.223-10483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 753,072 control chromosomes in the GnomAD database, including 8,134 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 0.15 ( 3752 hom., cov: 32)

Exomes 𝑓: 0.067 ( 4382 hom. )

Consequence

CCDC192
NM_001317938.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.80

Variant links:

Genes affected

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

CCDC192 links:

CUL1P1 (HGNC:49567): (cullin 1 pseudogene 1)

CUL1P1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2 linkuse as main transcript	c.223-10483G>A		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	Appris
CCDC192	ENST00000514853.5 linkuse as main transcript	c.223-10483G>A	intron_variant		5	NM_001317938.2	ENSP00000490579	A2
CUL1P1	ENST00000509510.1 linkuse as main transcript	n.423C>T	non_coding_transcript_exon_variant	1/1
CCDC192	ENST00000706942.1 linkuse as main transcript	c.280-10483G>A	intron_variant				ENSP00000516662	P4

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

22094

AN:

152062

Hom.:

3743

Cov.:

show subpopulations

Gnomad AFR

AF:

0.396

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.161

Gnomad ASJ

AF:

0.0963

Gnomad EAS

AF:

0.269

Gnomad SAS

AF:

0.0841

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0121

Gnomad OTH

AF:

0.130

GnomAD4 exome

AF:

0.0670

AC:

40264

AN:

600892

Hom.:

4382

Cov.:

AF XY:

0.0619

AC XY:

20273

AN XY:

327518

show subpopulations

Gnomad4 AFR exome

AF:

0.391

Gnomad4 AMR exome

AF:

0.225

Gnomad4 ASJ exome

AF:

0.107

Gnomad4 EAS exome

AF:

0.263

Gnomad4 SAS exome

AF:

0.0760

Gnomad4 FIN exome

AF:

0.00262

Gnomad4 NFE exome

AF:

0.0134

Gnomad4 OTH exome

AF:

0.0782

GnomAD4 genome

AF:

0.146

AC:

22146

AN:

152180

Hom.:

3752

Cov.:

AF XY:

0.145

AC XY:

10784

AN XY:

74426

show subpopulations

Gnomad4 AFR

AF:

0.396

Gnomad4 AMR

AF:

0.161

Gnomad4 ASJ

AF:

0.0963

Gnomad4 EAS

AF:

0.269

Gnomad4 SAS

AF:

0.0842

Gnomad4 FIN

AF:

0.00104

Gnomad4 NFE

AF:

0.0121

Gnomad4 OTH

AF:

0.132

Alfa

AF:

0.0591

Hom.:

198

Bravo

AF:

0.171

Asia WGS

AF:

0.209

AC:

727

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

2.1

DANN

Benign

0.77

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over