Genetic Variant CCDC192:c.411+5762G>A (chr5-127803924-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.95

Publications

5 publications found

Variant links:

Genes affected

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

CCDC192 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2 link	c.411+5762G>A		intron_variant	Intron 5 of 6	ENST00000514853.5	NP_001304867.2	P0DO97

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5 link	c.411+5762G>A		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1 link	c.468+5762G>A		intron_variant	Intron 5 of 6			ENSP00000516662.1		P0DO97

Frequencies

GnomAD3 genomes

AF:

0.0568

AC:

8645

AN:

152072

Hom.:

557

Cov.:

show subpopulations

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.:

AF XY:

0.0595

AC XY:

4425

AN XY:

74424

show subpopulations

African (AFR)

AF:

0.0889

AC:

3692

AN:

41508

American (AMR)

AF:

0.127

AC:

1936

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0954

AC:

331

AN:

3468

East Asian (EAS)

AF:

0.268

AC:

1387

AN:

5168

South Asian (SAS)

AF:

0.0770

AC:

371

AN:

4816

European-Finnish (FIN)

AF:

0.00104

AC:

AN:

10614

Middle Eastern (MID)

AF:

0.126

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0108

AC:

735

AN:

68004

Other (OTH)

AF:

0.0719

AC:

152

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

378

756

1133

1511

1889

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

192

288

384

480

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0323

Hom.:

736

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

(source)

DANN

Benign

0.44

PhyloP100

-2.9

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over