5-127833223-G-T

Position:

• chr5-127833223-G-T

Variant summary

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

The NM_001317938.2(CCDC192):​c.411+35061G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.401 in 151,880 control chromosomes in the GnomAD database, including 12,347 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 0.40 (12347 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.411+35061G>T		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+35061G>T		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.468+35061G>T		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60923 AN: 151760 Hom.: 12334 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.376

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.394

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

GnomAD4 genome AF: 0.401 AC: 60967 AN: 151880 Hom.: 12347 Cov.: 32 AF XY: 0.402 AC XY: 29800 AN XY: 74210

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.376

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.276

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.395

Alfa AF: 0.399 Hom.: 1524

Bravo AF: 0.402

Asia WGS AF: 0.376 AC: 1308 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.14
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9285907; hg19: chr5-127168915;