Genetic Variant CCDC190:c.*1784T>C (chr1-162852981-A-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001394065.1(CCDC190):c.*1784T>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 0.00000163 in 614,660 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 34)

Exomes 𝑓: 0.0000016 ( 0 hom. )

Consequence

CCDC190
NM_001394065.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.989

Publications

0 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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_001394065.1 link	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4	ENST00000367912.7	NP_001380994.1
CCDC190	NM_178550.6 link	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4		NP_848645.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC190	ENST00000367912.7 link	c.*1784T>C		3_prime_UTR_variant	Exon 4 of 4	5	NM_001394065.1	ENSP00000356888.3
CCDC190	ENST00000524691.1 link	n.152+2651T>C		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000163

AC:

AN:

614660

Hom.:

Cov.:

AF XY:

0.00000308

AC XY:

AN XY:

324240

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

15948

American (AMR)

AF:

0.00

AC:

AN:

29430

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

18102

East Asian (EAS)

AF:

0.00

AC:

AN:

31686

South Asian (SAS)

AF:

0.0000179

AC:

AN:

55792

European-Finnish (FIN)

AF:

0.00

AC:

AN:

46110

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3662

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

382210

Other (OTH)

AF:

0.00

AC:

AN:

31720

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.525

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.2

(source)

DANN

Benign

0.75

PhyloP100

-0.99

Mutation Taster

=100/0

polymorphism

(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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over