5-127851325-C-T

Variant names:

• chr5-127851325-C-T
• rs245195
• NM_001317938.2:c.412-24213C>T

Variant summary

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

The NM_001317938.2(CCDC192):​c.412-24213C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.659 in 152,084 control chromosomes in the GnomAD database, including 33,115 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 (33115 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 2 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-24213C>T		intron_variant	Intron 5 of 6	ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-24213C>T		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-24213C>T		intron_variant	Intron 5 of 6			ENSP00000516662.1
ENSG00000250603	ENST00000507509.1	n.191+6289G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.659 AC: 100167 AN: 151966 Hom.: 33094 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.614

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.716

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.659 AC: 100235 AN: 152084 Hom.: 33115 Cov.: 32 AF XY: 0.658 AC XY: 48906 AN XY: 74330

African (AFR) AF: 0.614 AC: 25491 AN: 41486

American (AMR) AF: 0.654 AC: 10007 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.614 AC: 2126 AN: 3464

East Asian (EAS) AF: 0.591 AC: 3059 AN: 5176

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4812

European-Finnish (FIN) AF: 0.716 AC: 7559 AN: 10554

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

European-Non Finnish (NFE) AF: 0.693 AC: 47100 AN: 67978

Other (OTH) AF: 0.638 AC: 1349 AN: 2114

Alfa AF: 0.675 Hom.: 21145

Bravo AF: 0.651

Asia WGS AF: 0.542 AC: 1887 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.36
DANN	Benign	0.59
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs245195; hg19: chr5-127187017;