5-127871843-G-A

Variant names:

• chr5-127871843-G-A
• rs245183
• NM_001317938.2:c.412-3695G>A

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-3695G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 152,050 control chromosomes in the GnomAD database, including 33,502 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 0.66 (33502 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 2 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=-0.69).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.692 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.412-3695G>A		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.412-3695G>A		intron	N/A	ENSP00000490579.2
	CCDC192	ENST00000706942.1		c.469-3695G>A		intron	N/A	ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 100705 AN: 151932 Hom.: 33477 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.588

Gnomad SAS AF: 0.540

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.697

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.663 AC: 100778 AN: 152050 Hom.: 33502 Cov.: 32 AF XY: 0.661 AC XY: 49084 AN XY: 74300

African (AFR) AF: 0.626 AC: 25944 AN: 41444

American (AMR) AF: 0.655 AC: 10005 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2126 AN: 3468

East Asian (EAS) AF: 0.588 AC: 3046 AN: 5182

South Asian (SAS) AF: 0.542 AC: 2606 AN: 4812

European-Finnish (FIN) AF: 0.699 AC: 7387 AN: 10572

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.697 AC: 47374 AN: 67974

Other (OTH) AF: 0.644 AC: 1360 AN: 2112

Alfa AF: 0.681 Hom.: 16385

Bravo AF: 0.656

Asia WGS AF: 0.542 AC: 1886 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	11
DANN	Benign	0.83
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs245183; hg19: chr5-127207535;