5-127786620-G-A

Position:

• chr5-127786620-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001317938.2(CCDC192):​c.223-10483G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0829 in 753,072 control chromosomes in the GnomAD database, including 8,134 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 0.15 (3752 hom., cov: 32)
  • Exomes 𝑓: 0.067 (4382 hom.)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.80

Genes affected

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

CUL1P1 (HGNC:49567): (cullin 1 pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.51).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.391 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC192	NM_001317938.2	c.223-10483G>A		intron_variant		ENST00000514853.5	NP_001304867.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC192	ENST00000514853.5	c.223-10483G>A		intron_variant		5	NM_001317938.2	ENSP00000490579	A2
CUL1P1	ENST00000509510.1	n.423C>T		non_coding_transcript_exon_variant	1/1
CCDC192	ENST00000706942.1	c.280-10483G>A		intron_variant				ENSP00000516662	P4

Frequencies

GnomAD3 genomes AF: 0.145 AC: 22094 AN: 152062 Hom.: 3743 Cov.: 32

Gnomad AFR AF: 0.396

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.161

Gnomad ASJ AF: 0.0963

Gnomad EAS AF: 0.269

Gnomad SAS AF: 0.0841

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0121

Gnomad OTH AF: 0.130

GnomAD4 exome AF: 0.0670 AC: 40264 AN: 600892 Hom.: 4382 Cov.: 0 AF XY: 0.0619 AC XY: 20273 AN XY: 327518

Gnomad4 AFR exome AF: 0.391

Gnomad4 AMR exome AF: 0.225

Gnomad4 ASJ exome AF: 0.107

Gnomad4 EAS exome AF: 0.263

Gnomad4 SAS exome AF: 0.0760

Gnomad4 FIN exome AF: 0.00262

Gnomad4 NFE exome AF: 0.0134

Gnomad4 OTH exome AF: 0.0782

GnomAD4 genome AF: 0.146 AC: 22146 AN: 152180 Hom.: 3752 Cov.: 32 AF XY: 0.145 AC XY: 10784 AN XY: 74426

Gnomad4 AFR AF: 0.396

Gnomad4 AMR AF: 0.161

Gnomad4 ASJ AF: 0.0963

Gnomad4 EAS AF: 0.269

Gnomad4 SAS AF: 0.0842

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.0121

Gnomad4 OTH AF: 0.132

Alfa AF: 0.0591 Hom.: 198

Bravo AF: 0.171

Asia WGS AF: 0.209 AC: 727 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.51
CADD	Benign	2.1
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10463833; hg19: chr5-127122312; COSMIC: COSV72618160;