22-28778782-C-A

Variant names:

• chr22-28778782-C-A
• rs5762788
• NM_173510.4:c.240-2166C>A

Variant summary

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

The NM_173510.4(CCDC117):​c.240-2166C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,944 control chromosomes in the GnomAD database, including 13,190 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 (13190 hom., cov: 32)
• Consequence: CCDC117 NM_173510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.126
• Publications: 17 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC117	NM_173510.4	c.240-2166C>A		intron_variant	Intron 2 of 4	ENST00000249064.9	NP_775781.1
CCDC117	NM_001284263.2	c.186-2166C>A		intron_variant	Intron 1 of 3		NP_001271192.1
CCDC117	NM_001284264.2	c.240-4726C>A		intron_variant	Intron 2 of 3		NP_001271193.1
CCDC117	NM_001284265.1	c.-157-2166C>A		intron_variant	Intron 2 of 4		NP_001271194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC117	ENST00000249064.9	c.240-2166C>A		intron_variant	Intron 2 of 4	1	NM_173510.4	ENSP00000249064.4

Frequencies

GnomAD3 genomes AF: 0.396 AC: 60125 AN: 151826 Hom.: 13161 Cov.: 32

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.295

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.367

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

GnomAD4 genome AF: 0.396 AC: 60210 AN: 151944 Hom.: 13190 Cov.: 32 AF XY: 0.400 AC XY: 29727 AN XY: 74266

African (AFR) AF: 0.548 AC: 22679 AN: 41412

American (AMR) AF: 0.296 AC: 4516 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1139 AN: 3468

East Asian (EAS) AF: 0.675 AC: 3493 AN: 5174

South Asian (SAS) AF: 0.536 AC: 2583 AN: 4818

European-Finnish (FIN) AF: 0.373 AC: 3919 AN: 10512

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.306 AC: 20828 AN: 67966

Other (OTH) AF: 0.372 AC: 785 AN: 2110

Alfa AF: 0.332 Hom.: 38869

Bravo AF: 0.394

Asia WGS AF: 0.611 AC: 2126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.6
DANN	Benign	0.65
PhyloP100		0.13
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: rs5762788; hg19: chr22-29174770;