chr5-127816284-A-G

Variant names:

• chr5-127816284-A-G
• rs1421746
• NM_001317938.2:c.411+18122A>G

Variant summary

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

The NM_001317938.2(CCDC192):​c.411+18122A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.448 in 151,956 control chromosomes in the GnomAD database, including 16,698 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 0.45 (16698 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.103
• Publications: 8 publications found

Genes affected

CCDC192 (HGNC:49566): (coiled-coil domain containing 192)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001317938.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	NM_001317938.2	MANE Select	c.411+18122A>G		intron	N/A	NP_001304867.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.411+18122A>G		intron	N/A	ENSP00000490579.2
	CCDC192	ENST00000706942.1		c.468+18122A>G		intron	N/A	ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.448 AC: 68042 AN: 151838 Hom.: 16669 Cov.: 31

Gnomad AFR AF: 0.653

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.428

Gnomad ASJ AF: 0.418

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.353

Gnomad OTH AF: 0.440

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.448 AC: 68122 AN: 151956 Hom.: 16698 Cov.: 31 AF XY: 0.445 AC XY: 33055 AN XY: 74256

African (AFR) AF: 0.653 AC: 27072 AN: 41430

American (AMR) AF: 0.427 AC: 6528 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.418 AC: 1449 AN: 3466

East Asian (EAS) AF: 0.486 AC: 2507 AN: 5158

South Asian (SAS) AF: 0.254 AC: 1222 AN: 4812

European-Finnish (FIN) AF: 0.372 AC: 3934 AN: 10570

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.353 AC: 23978 AN: 67932

Other (OTH) AF: 0.439 AC: 927 AN: 2114

Alfa AF: 0.380 Hom.: 52798

Bravo AF: 0.464

Asia WGS AF: 0.396 AC: 1380 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.99
DANN	Benign	0.73
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs1421746; hg19: chr5-127151976;