rs5762795

chr22-28786512-C-Achr22-28786512-C-Gchr22-28786512-C-T

Variant summary

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

The NM_173510.4(CCDC117):c.*186C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.387 in 551,592 control chromosomes in the GnomAD database, including 46,522 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 0.43 (15906 hom., cov: 32)
  • Exomes 𝑓: 0.37 (30616 hom.)
• Consequence: CCDC117 NM_173510.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.46

Genes affected

CCDC117 (HGNC:26599): (coiled-coil domain containing 117)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.657 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC117	NM_173510.4	c.*186C>A		3_prime_UTR_variant	5/5	ENST00000249064.9
CCDC117	NM_001284263.2	c.*186C>A		3_prime_UTR_variant	4/4
CCDC117	NM_001284264.2	c.*186C>A		3_prime_UTR_variant	4/4
CCDC117	NM_001284265.1	c.*186C>A		3_prime_UTR_variant	5/5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC117	ENST00000249064.9	c.*186C>A		3_prime_UTR_variant	5/5	1	NM_173510.4	P1
CCDC117	ENST00000421503.6	c.*186C>A		3_prime_UTR_variant	4/4	2
CCDC117	ENST00000448492.6	c.*186C>A		3_prime_UTR_variant	4/4	2

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64823 AN: 151770 Hom.: 15857 Cov.: 32

Gnomad AFR AF: 0.652

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.308

Gnomad OTH AF: 0.391

GnomAD4 exome AF: 0.372 AC: 148782 AN: 399704 Hom.: 30616 Cov.: 4 AF XY: 0.377 AC XY: 78822 AN XY: 209352

Gnomad4 AFR exome AF: 0.653

Gnomad4 AMR exome AF: 0.325

Gnomad4 ASJ exome AF: 0.311

Gnomad4 EAS exome AF: 0.678

Gnomad4 SAS exome AF: 0.504

Gnomad4 FIN exome AF: 0.377

Gnomad4 NFE exome AF: 0.309

Gnomad4 OTH exome AF: 0.374

GnomAD4 genome AF: 0.428 AC: 64936 AN: 151888 Hom.: 15906 Cov.: 32 AF XY: 0.430 AC XY: 31890 AN XY: 74210

Gnomad4 AFR AF: 0.652

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.308

Gnomad4 OTH AF: 0.396

Alfa AF: 0.319 Hom.: 13698

Bravo AF: 0.429

Asia WGS AF: 0.616 AC: 2143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
Cadd	Benign	15
Dann	Benign	0.61
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs5762795; hg19: chr22-29182500; COSMIC: COSV50771760; COSMIC: COSV50771760;