22-28784010-C-T

Variant names:

• chr22-28784010-C-T
• rs5752797
• NM_173510.4:c.602+365C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_173510.4(CCDC117):​c.602+365C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.255 in 152,044 control chromosomes in the GnomAD database, including 5,720 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 0.26 (5720 hom., cov: 32)
• Consequence: CCDC117 NM_173510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.272
• Publications: 7 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.467 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC117	NM_173510.4	c.602+365C>T		intron_variant	Intron 4 of 4	ENST00000249064.9	NP_775781.1
CCDC117	NM_001284263.2	c.548+365C>T		intron_variant	Intron 3 of 3		NP_001271192.1
CCDC117	NM_001284264.2	c.377+365C>T		intron_variant	Intron 3 of 3		NP_001271193.1
CCDC117	NM_001284265.1	c.206+365C>T		intron_variant	Intron 4 of 4		NP_001271194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC117	ENST00000249064.9	c.602+365C>T		intron_variant	Intron 4 of 4	1	NM_173510.4	ENSP00000249064.4

Frequencies

GnomAD3 genomes AF: 0.255 AC: 38730 AN: 151926 Hom.: 5704 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.197

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.346

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.255 AC: 38793 AN: 152044 Hom.: 5720 Cov.: 32 AF XY: 0.255 AC XY: 18973 AN XY: 74318

African (AFR) AF: 0.375 AC: 15561 AN: 41466

American (AMR) AF: 0.198 AC: 3016 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3470

East Asian (EAS) AF: 0.483 AC: 2497 AN: 5172

South Asian (SAS) AF: 0.346 AC: 1669 AN: 4820

European-Finnish (FIN) AF: 0.173 AC: 1822 AN: 10554

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12770 AN: 67986

Other (OTH) AF: 0.259 AC: 547 AN: 2108

Alfa AF: 0.176 Hom.: 1141

Bravo AF: 0.263

Asia WGS AF: 0.432 AC: 1501 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.48
PhyloP100		-0.27
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs5752797; hg19: chr22-29179998;