Genetic Variant CCDC190:c.-13+1593T>G (chr1-162867060-A-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_178550.6(CCDC190):c.-13+1593T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.857 in 151,786 control chromosomes in the GnomAD database, including 56,964 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 0.86 ( 56964 hom., cov: 31)

Consequence

CCDC190
NM_178550.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.987

Publications

3 publications found

Variant links:

Genes affected

CCDC190 (HGNC:28736): (coiled-coil domain containing 190)

CCDC190 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=-1.01).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_178550.6 link	c.-13+1593T>G		intron_variant	Intron 1 of 3		NP_848645.3	Q86UF4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC190	ENST00000367910.5 link	c.-13+1593T>G		intron_variant	Intron 1 of 3	2		ENSP00000356886.1		Q86UF4-1

Frequencies

GnomAD3 genomes

AF:

0.857

AC:

130046

AN:

151672

Hom.:

56961

Cov.:

show subpopulations

Gnomad AFR

AF:

0.741

Gnomad AMI

AF:

0.942

Gnomad AMR

AF:

0.806

Gnomad ASJ

AF:

0.947

Gnomad EAS

AF:

0.430

Gnomad SAS

AF:

0.801

Gnomad FIN

AF:

0.951

Gnomad MID

AF:

0.911

Gnomad NFE

AF:

0.956

Gnomad OTH

AF:

0.864

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

GnomAD4 genome

AF:

0.857

AC:

130102

AN:

151786

Hom.:

56964

Cov.:

AF XY:

0.853

AC XY:

63283

AN XY:

74186

show subpopulations

African (AFR)

AF:

0.741

AC:

30678

AN:

41402

American (AMR)

AF:

0.805

AC:

12274

AN:

15250

Ashkenazi Jewish (ASJ)

AF:

0.947

AC:

3287

AN:

3472

East Asian (EAS)

AF:

0.431

AC:

2224

AN:

5162

South Asian (SAS)

AF:

0.801

AC:

3855

AN:

4810

European-Finnish (FIN)

AF:

0.951

AC:

9941

AN:

10458

Middle Eastern (MID)

AF:

0.908

AC:

267

AN:

294

European-Non Finnish (NFE)

AF:

0.956

AC:

64905

AN:

67922

Other (OTH)

AF:

0.861

AC:

1812

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

818

1635

2453

3270

4088

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

874

1748

2622

3496

4370

<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:

0.884

Hom.:

9595

Bravo

AF:

0.839

Asia WGS

AF:

0.599

AC:

2051

AN:

3424

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

2.4

(source)

DANN

Benign

0.51

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism (auto)

(source)

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