rs151849

Positions:

• chr5-127834951-A-G
• chr5-127834951-A-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+36789A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 152,124 control chromosomes in the GnomAD database, including 6,642 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 0.29 (6642 hom., cov: 32)
• Consequence: CCDC192 NM_001317938.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.467

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=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC192	NM_001317938.2	c.411+36789A>G		intron_variant		ENST00000514853.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC192	ENST00000514853.5	c.411+36789A>G		intron_variant		5	NM_001317938.2	A2
CCDC192	ENST00000706942.1	c.468+36789A>G		intron_variant				P4

Frequencies

GnomAD3 genomes AF: 0.292 AC: 44370 AN: 152006 Hom.: 6644 Cov.: 32

Gnomad AFR AF: 0.222

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.330

Gnomad ASJ AF: 0.386

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.292 AC: 44376 AN: 152124 Hom.: 6642 Cov.: 32 AF XY: 0.295 AC XY: 21911 AN XY: 74340

Gnomad4 AFR AF: 0.221

Gnomad4 AMR AF: 0.330

Gnomad4 ASJ AF: 0.386

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.452

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.328

Alfa AF: 0.282 Hom.: 4280

Bravo AF: 0.294

Asia WGS AF: 0.433 AC: 1503 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.1
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs151849; hg19: chr5-127170643;