5-127828763-C-T

Variant names:

• chr5-127828763-C-T
• rs245314
• NM_001317938.2:c.411+30601C>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.411+30601C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.359 in 151,892 control chromosomes in the GnomAD database, including 10,114 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 0.36 (10114 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.107
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.411+30601C>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.411+30601C>T		intron_variant	Intron 5 of 6	5	NM_001317938.2	ENSP00000490579.2
CCDC192	ENST00000706942.1	c.468+30601C>T		intron_variant	Intron 5 of 6			ENSP00000516662.1

Frequencies

GnomAD3 genomes AF: 0.359 AC: 54495 AN: 151774 Hom.: 10101 Cov.: 32

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.285

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.374

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

GnomAD4 genome AF: 0.359 AC: 54547 AN: 151892 Hom.: 10114 Cov.: 32 AF XY: 0.360 AC XY: 26696 AN XY: 74228

African (AFR) AF: 0.450 AC: 18614 AN: 41406

American (AMR) AF: 0.354 AC: 5404 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1335 AN: 3466

East Asian (EAS) AF: 0.462 AC: 2384 AN: 5164

South Asian (SAS) AF: 0.458 AC: 2207 AN: 4814

European-Finnish (FIN) AF: 0.285 AC: 3000 AN: 10544

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20545 AN: 67922

Other (OTH) AF: 0.374 AC: 787 AN: 2104

Alfa AF: 0.340 Hom.: 1628

Bravo AF: 0.370

Asia WGS AF: 0.478 AC: 1661 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs245314; hg19: chr5-127164455;