chr1-162852981-A-C

Variant names:

• chr1-162852981-A-C
• rs2684878
• NM_001394065.1:c.*1784T>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.989
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394065.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC190	NM_001394065.1	MANE Select	c.*1784T>G		3_prime_UTR	Exon 4 of 4	NP_001380994.1	A0A8J8YXK0
	CCDC190	NM_178550.6		c.*1784T>G		3_prime_UTR	Exon 4 of 4	NP_848645.3	Q86UF4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC190	ENST00000367912.7	TSL:5 MANE Select	c.*1784T>G		3_prime_UTR	Exon 4 of 4	ENSP00000356888.3	A0A8J8YXK0
	CCDC190	ENST00000524691.1	TSL:1	n.152+2651T>G		intron	N/A
	CCDC190	ENST00000876170.1		c.*1784T>G		3_prime_UTR	Exon 4 of 4	ENSP00000546229.1

Frequencies

GnomAD3 genomes AF: 0.863 AC: 131284 AN: 152166 Hom.: 57116 Cov.: 34

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

GnomAD2 exomes AF: 0.836 AC: 101101 AN: 120890 AF XY: 0.841

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 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.: 8 AF XY: 0.874 AC XY: 283116 AN XY: 323986

African (AFR) AF: 0.829 AC: 13202 AN: 15932

American (AMR) AF: 0.739 AC: 21712 AN: 29378

Ashkenazi Jewish (ASJ) AF: 0.906 AC: 16379 AN: 18082

East Asian (EAS) AF: 0.566 AC: 17921 AN: 31670

South Asian (SAS) AF: 0.792 AC: 44136 AN: 55700

European-Finnish (FIN) AF: 0.917 AC: 42257 AN: 46088

Middle Eastern (MID) AF: 0.874 AC: 3195 AN: 3656

European-Non Finnish (NFE) AF: 0.920 AC: 351409 AN: 381956

Other (OTH) AF: 0.872 AC: 27635 AN: 31700

GnomAD4 genome AF: 0.863 AC: 131365 AN: 152286 Hom.: 57142 Cov.: 34 AF XY: 0.859 AC XY: 63982 AN XY: 74468

African (AFR) AF: 0.822 AC: 34125 AN: 41538

American (AMR) AF: 0.803 AC: 12281 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3127 AN: 3472

East Asian (EAS) AF: 0.561 AC: 2905 AN: 5180

South Asian (SAS) AF: 0.783 AC: 3781 AN: 4826

European-Finnish (FIN) AF: 0.914 AC: 9711 AN: 10620

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.918 AC: 62474 AN: 68032

Other (OTH) AF: 0.863 AC: 1825 AN: 2114

Alfa AF: 0.875 Hom.: 15356

Bravo AF: 0.850

Asia WGS AF: 0.663 AC: 2307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.50
PhyloP100		-0.99
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs2684878; hg19: chr1-162822771;