Genetic Variant NM_001317938.2:c.223-7033T>C (chr5-127790070-T-C) – 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.223-7033T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.143 in 152,214 control chromosomes in the GnomAD database, including 3,591 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 0.14 ( 3591 hom., cov: 33)

Consequence

CCDC192
NM_001317938.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.214

Publications

3 publications found

Variant links:

Genes affected

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

CCDC192 links:

Genome browser will be placed here

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=-0.74).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2 link	c.223-7033T>C		intron_variant	Intron 3 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.223-7033T>C		intron_variant	Intron 3 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1 link	c.280-7033T>C		intron_variant	Intron 3 of 6			ENSP00000516662.1		P0DO97

Frequencies

GnomAD3 genomes

AF:

0.142

AC:

21656

AN:

152096

Hom.:

3582

Cov.:

show subpopulations

Gnomad AFR

AF:

0.386

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.159

Gnomad ASJ

AF:

0.0961

Gnomad EAS

AF:

0.268

Gnomad SAS

AF:

0.0782

Gnomad FIN

AF:

0.00104

Gnomad MID

AF:

0.149

Gnomad NFE

AF:

0.0120

Gnomad OTH

AF:

0.127

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

GnomAD4 genome

AF:

0.143

AC:

21705

AN:

152214

Hom.:

3591

Cov.:

AF XY:

0.142

AC XY:

10565

AN XY:

74450

show subpopulations

African (AFR)

AF:

0.386

AC:

16032

AN:

41504

American (AMR)

AF:

0.159

AC:

2432

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0961

AC:

333

AN:

3466

East Asian (EAS)

AF:

0.268

AC:

1387

AN:

5172

South Asian (SAS)

AF:

0.0782

AC:

377

AN:

4820

European-Finnish (FIN)

AF:

0.00104

AC:

AN:

10622

Middle Eastern (MID)

AF:

0.143

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0120

AC:

818

AN:

68020

Other (OTH)

AF:

0.129

AC:

273

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

742

1484

2225

2967

3709

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

204

408

612

816

1020

<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:

0.0754

Hom.:

2859

Bravo

AF:

0.168

Asia WGS

AF:

0.197

AC:

686

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

4.5

(source)

DANN

Benign

0.88

PhyloP100

0.21

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