NM_173510.4:c.464+1154G>A

Variant names:

• chr22-28782326-G-A
• rs6005879
• NM_173510.4:c.464+1154G>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.464+1154G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.119 in 143,886 control chromosomes in the GnomAD database, including 1,453 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 0.12 (1453 hom., cov: 28)
• Consequence: CCDC117 NM_173510.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 3 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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_173510.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC117	NM_173510.4	MANE Select	c.464+1154G>A		intron	N/A	NP_775781.1
	CCDC117	NM_001284263.2		c.410+1154G>A		intron	N/A	NP_001271192.1
	CCDC117	NM_001284264.2		c.240-1182G>A		intron	N/A	NP_001271193.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC117	ENST00000249064.9	TSL:1 MANE Select	c.464+1154G>A		intron	N/A	ENSP00000249064.4
	CCDC117	ENST00000936868.1		c.581+1154G>A		intron	N/A	ENSP00000606927.1
	CCDC117	ENST00000936867.1		c.464+1154G>A		intron	N/A	ENSP00000606926.1

Frequencies

GnomAD3 genomes AF: 0.119 AC: 17072 AN: 143784 Hom.: 1447 Cov.: 28

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.0533

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0718

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.0669

Gnomad FIN AF: 0.0805

Gnomad MID AF: 0.0833

Gnomad NFE AF: 0.0547

Gnomad OTH AF: 0.0977

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

GnomAD4 genome AF: 0.119 AC: 17119 AN: 143886 Hom.: 1453 Cov.: 28 AF XY: 0.120 AC XY: 8309 AN XY: 69372

African (AFR) AF: 0.234 AC: 9016 AN: 38544

American (AMR) AF: 0.112 AC: 1535 AN: 13738

Ashkenazi Jewish (ASJ) AF: 0.0718 AC: 246 AN: 3428

East Asian (EAS) AF: 0.284 AC: 1382 AN: 4858

South Asian (SAS) AF: 0.0672 AC: 304 AN: 4522

European-Finnish (FIN) AF: 0.0805 AC: 710 AN: 8816

Middle Eastern (MID) AF: 0.0752 AC: 20 AN: 266

European-Non Finnish (NFE) AF: 0.0547 AC: 3657 AN: 66828

Other (OTH) AF: 0.101 AC: 201 AN: 1986

Alfa AF: 0.0882 Hom.: 127

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.24
PhyloP100		0.17
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: rs6005879; hg19: chr22-29178314;