rs2805050

Variant names:

• chr1-162867060-A-C
• rs2805050
• NM_178550.6:c.-13+1593T>G

Variant summary

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

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.987
• Publications: 3 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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_178550.6. 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_178550.6		c.-13+1593T>G		intron	N/A	NP_848645.3	Q86UF4-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC190	ENST00000367910.5	TSL:2	c.-13+1593T>G		intron	N/A	ENSP00000356886.1	Q86UF4-1
	CCDC190	ENST00000876170.1		c.-13+1593T>G		intron	N/A	ENSP00000546229.1

Frequencies

GnomAD3 genomes AF: 0.857 AC: 130046 AN: 151672 Hom.: 56961 Cov.: 31

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.: 31 AF XY: 0.853 AC XY: 63283 AN XY: 74186

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

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.4
DANN	Benign	0.51
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: rs2805050; hg19: chr1-162836850;