5-127853881-A-G

Variant names:

• chr5-127853881-A-G
• rs245191
• NM_001317938.2:c.412-21657A>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.412-21657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.678 in 151,988 control chromosomes in the GnomAD database, including 34,936 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 0.68 (34936 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 1 publications found

Genes affected

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

ENSG00000250603 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	NM_001317938.2	MANE Select	c.412-21657A>G		intron	N/A	NP_001304867.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC192	ENST00000514853.5	TSL:5 MANE Select	c.412-21657A>G		intron	N/A	ENSP00000490579.2
	CCDC192	ENST00000706942.1		c.469-21657A>G		intron	N/A	ENSP00000516662.1
	ENSG00000250603	ENST00000507509.1	TSL:2	n.191+3733T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.678 AC: 102965 AN: 151870 Hom.: 34906 Cov.: 31

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.717

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.654

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

GnomAD4 genome AF: 0.678 AC: 103054 AN: 151988 Hom.: 34936 Cov.: 31 AF XY: 0.677 AC XY: 50281 AN XY: 74268

African (AFR) AF: 0.679 AC: 28145 AN: 41436

American (AMR) AF: 0.661 AC: 10103 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2128 AN: 3470

East Asian (EAS) AF: 0.591 AC: 3050 AN: 5160

South Asian (SAS) AF: 0.546 AC: 2625 AN: 4806

European-Finnish (FIN) AF: 0.717 AC: 7562 AN: 10548

Middle Eastern (MID) AF: 0.575 AC: 168 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47133 AN: 67976

Other (OTH) AF: 0.653 AC: 1377 AN: 2108

Alfa AF: 0.690 Hom.: 4714

Bravo AF: 0.672

Asia WGS AF: 0.556 AC: 1934 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.50
DANN	Benign	0.30
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs245191; hg19: chr5-127189573;