5-127867500-C-T

Variant names:

• chr5-127867500-C-T
• rs245178
• NM_001317938.2:c.412-8038C>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.412-8038C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 152,164 control chromosomes in the GnomAD database, including 42,206 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 0.74 (42206 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.87 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.412-8038C>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.412-8038C>T		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.469-8038C>T		intron_variant	Intron 5 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.739 AC: 112340 AN: 152046 Hom.: 42155 Cov.: 32

Gnomad AFR AF: 0.878

Gnomad AMI AF: 0.837

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.665

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.550

Gnomad FIN AF: 0.698

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.699

Gnomad OTH AF: 0.714

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

GnomAD4 genome AF: 0.739 AC: 112454 AN: 152164 Hom.: 42206 Cov.: 32 AF XY: 0.735 AC XY: 54656 AN XY: 74378

African (AFR) AF: 0.878 AC: 36470 AN: 41536

American (AMR) AF: 0.695 AC: 10612 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.665 AC: 2306 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3049 AN: 5172

South Asian (SAS) AF: 0.551 AC: 2655 AN: 4818

European-Finnish (FIN) AF: 0.698 AC: 7385 AN: 10578

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.699 AC: 47514 AN: 67996

Other (OTH) AF: 0.714 AC: 1507 AN: 2112

Alfa AF: 0.699 Hom.: 59588

Bravo AF: 0.743

Asia WGS AF: 0.575 AC: 2003 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.57
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs245178; hg19: chr5-127203192;