5-127839739-G-A

Position:

• chr5-127839739-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.412-35799G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 151,802 control chromosomes in the GnomAD database, including 8,479 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 0.32 (8479 hom., cov: 31)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.342

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.396 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.412-35799G>A		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.412-35799G>A		intron_variant		5	NM_001317938.2	A2
	ENST00000507509.1	n.192-1057C>T		intron_variant, non_coding_transcript_variant		2
CCDC192	ENST00000706942.1	c.469-35799G>A		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48596 AN: 151684 Hom.: 8474 Cov.: 31

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.475

Gnomad AMR AF: 0.298

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.321

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

GnomAD4 genome AF: 0.320 AC: 48609 AN: 151802 Hom.: 8479 Cov.: 31 AF XY: 0.318 AC XY: 23603 AN XY: 74194

Gnomad4 AFR AF: 0.191

Gnomad4 AMR AF: 0.298

Gnomad4 ASJ AF: 0.314

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.194

Gnomad4 FIN AF: 0.426

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.317

Alfa AF: 0.367 Hom.: 5787

Bravo AF: 0.307

Asia WGS AF: 0.200 AC: 699 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.8
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6874357; hg19: chr5-127175431;