Genetic Variant NM_001394065.1:c.*1784T>G (chr1-162852981-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001394065.1(CCDC190):c.*1784T>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.873 in 766,448 control chromosomes in the GnomAD database, including 295,420 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 ( 57142 hom., cov: 34)

Exomes 𝑓: 0.88 ( 238278 hom. )

Consequence

CCDC190
NM_001394065.1 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.989

Variant links:

Genes affected

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

CCDC190 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC190	NM_001394065.1 link	c.*1784T>G		3_prime_UTR_variant	Exon 4 of 4	ENST00000367912.7	NP_001380994.1
CCDC190	NM_178550.6 link	c.*1784T>G		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 link	c.*1784T>G		3_prime_UTR_variant	Exon 4 of 4	5	NM_001394065.1	ENSP00000356888.3		A0A8J8YXK0
CCDC190	ENST00000524691.1 link	n.152+2651T>G		intron_variant	Intron 1 of 1	1

Frequencies

GnomAD3 genomes

AF:

0.863

AC:

131284

AN:

152166

Hom.:

57116

Cov.:

show subpopulations

Gnomad AFR

AF:

0.822

Gnomad AMI

AF:

0.971

Gnomad AMR

AF:

0.804

Gnomad ASJ

AF:

0.901

Gnomad EAS

AF:

0.561

Gnomad SAS

AF:

0.783

Gnomad FIN

AF:

0.914

Gnomad MID

AF:

0.861

Gnomad NFE

AF:

0.918

Gnomad OTH

AF:

0.863

GnomAD3 exomes

AF:

0.836

AC:

101101

AN:

120890

Hom.:

43104

AF XY:

0.841

AC XY:

53909

AN XY:

64098

show subpopulations

Gnomad AFR exome

AF:

0.823

Gnomad AMR exome

AF:

0.731

Gnomad ASJ exome

AF:

0.905

Gnomad EAS exome

AF:

0.569

Gnomad SAS exome

AF:

0.792

Gnomad FIN exome

AF:

0.917

Gnomad NFE exome

AF:

0.919

Gnomad OTH exome

AF:

0.868

GnomAD4 exome

AF:

0.876

AC:

537846

AN:

614162

Hom.:

238278

Cov.:

AF XY:

0.874

AC XY:

283116

AN XY:

323986

show subpopulations

Gnomad4 AFR exome

AF:

0.829

Gnomad4 AMR exome

AF:

0.739

Gnomad4 ASJ exome

AF:

0.906

Gnomad4 EAS exome

AF:

0.566

Gnomad4 SAS exome

AF:

0.792

Gnomad4 FIN exome

AF:

0.917

Gnomad4 NFE exome

AF:

0.920

Gnomad4 OTH exome

AF:

0.872

GnomAD4 genome

AF:

0.863

AC:

131365

AN:

152286

Hom.:

57142

Cov.:

AF XY:

0.859

AC XY:

63982

AN XY:

74468

show subpopulations

Gnomad4 AFR

AF:

0.822

Gnomad4 AMR

AF:

0.803

Gnomad4 ASJ

AF:

0.901

Gnomad4 EAS

AF:

0.561

Gnomad4 SAS

AF:

0.783

Gnomad4 FIN

AF:

0.914

Gnomad4 NFE

AF:

0.918

Gnomad4 OTH

AF:

0.863

Alfa

AF:

0.876

Hom.:

15080

Bravo

AF:

0.850

Asia WGS

AF:

0.663

AC:

2307

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.1

DANN

Benign

0.50

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over