Genetic Variant CCDC190:c.*3264T>C (chr1-162851501-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001394065.1(CCDC190):c.*3264T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.573 in 151,392 control chromosomes in the GnomAD database, including 24,977 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 0.57 ( 24967 hom., cov: 28)

Exomes 𝑓: 0.68 ( 10 hom. )

Consequence

CCDC190
NM_001394065.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.362

Publications

12 publications found

Variant links:

Genes affected

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

CCDC190 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=-0.88).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.612 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_001394065.1 link	c.*3264T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000367912.7	NP_001380994.1
CCDC190	NM_178550.6 link	c.*3264T>C		3_prime_UTR_variant	Exon 4 of 4		NP_848645.3	Q86UF4-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC190	ENST00000367912.7 link	c.*3264T>C		3_prime_UTR_variant	Exon 4 of 4	5	NM_001394065.1	ENSP00000356888.3		A0A8J8YXK0
CCDC190	ENST00000524691.1 link	n.152+4131T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.573

AC:

86653

AN:

151230

Hom.:

24957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.538

Gnomad AMI

AF:

0.575

Gnomad AMR

AF:

0.557

Gnomad ASJ

AF:

0.633

Gnomad EAS

AF:

0.425

Gnomad SAS

AF:

0.632

Gnomad FIN

AF:

0.572

Gnomad MID

AF:

0.573

Gnomad NFE

AF:

0.602

Gnomad OTH

AF:

0.571

GnomAD4 exome

AF:

0.682

AC:

AN:

Hom.:

Cov.:

AF XY:

0.706

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.500

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AF:

1.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.530

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.573

AC:

86702

AN:

151348

Hom.:

24967

Cov.:

AF XY:

0.573

AC XY:

42354

AN XY:

73914

show subpopulations

African (AFR)

AF:

0.538

AC:

22154

AN:

41160

American (AMR)

AF:

0.557

AC:

8477

AN:

15222

Ashkenazi Jewish (ASJ)

AF:

0.633

AC:

2195

AN:

3470

East Asian (EAS)

AF:

0.425

AC:

2180

AN:

5128

South Asian (SAS)

AF:

0.631

AC:

3026

AN:

4794

European-Finnish (FIN)

AF:

0.572

AC:

5978

AN:

10444

Middle Eastern (MID)

AF:

0.561

AC:

165

AN:

294

European-Non Finnish (NFE)

AF:

0.602

AC:

40806

AN:

67834

Other (OTH)

AF:

0.573

AC:

1200

AN:

2096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1817

3633

5450

7266

9083

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

744

1488

2232

2976

3720

<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:

0.591

Hom.:

89301

Bravo

AF:

0.567

Asia WGS

AF:

0.520

AC:

1807

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

1.4

(source)

DANN

Benign

0.86

PhyloP100

-0.36

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over