5-127804274-A-G

Variant names:

• chr5-127804274-A-G
• rs10519960
• NM_001317938.2:c.411+6112A>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+6112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,084 control chromosomes in the GnomAD database, including 6,726 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 0.28 (6726 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.223
• Publications: 3 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=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.418 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+6112A>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+6112A>G		intron	N/A	ENSP00000490579.2
	CCDC192	ENST00000706942.1		c.468+6112A>G		intron	N/A	ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42585 AN: 151966 Hom.: 6726 Cov.: 32

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.311

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.332

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.280 AC: 42594 AN: 152084 Hom.: 6726 Cov.: 32 AF XY: 0.284 AC XY: 21108 AN XY: 74348

African (AFR) AF: 0.123 AC: 5117 AN: 41522

American (AMR) AF: 0.341 AC: 5204 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.322 AC: 1114 AN: 3462

East Asian (EAS) AF: 0.380 AC: 1962 AN: 5160

South Asian (SAS) AF: 0.434 AC: 2094 AN: 4828

European-Finnish (FIN) AF: 0.336 AC: 3545 AN: 10564

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.332 AC: 22541 AN: 67966

Other (OTH) AF: 0.307 AC: 649 AN: 2112

Alfa AF: 0.225 Hom.: 787

Bravo AF: 0.276

Asia WGS AF: 0.408 AC: 1417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.5
DANN	Benign	0.77
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs10519960; hg19: chr5-127139966; COSMIC: COSV72617357;