rs6005879

Positions:

• chr22-28782326-G-A
• chr22-28782326-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC117	NM_173510.4	c.464+1154G>A		intron_variant		ENST00000249064.9
CCDC117	NM_001284263.2	c.410+1154G>A		intron_variant
CCDC117	NM_001284264.2	c.240-1182G>A		intron_variant
CCDC117	NM_001284265.1	c.68+1154G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC117	ENST00000249064.9	c.464+1154G>A		intron_variant		1	NM_173510.4	P1

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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0718

Gnomad4 EAS AF: 0.284

Gnomad4 SAS AF: 0.0672

Gnomad4 FIN AF: 0.0805

Gnomad4 NFE AF: 0.0547

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0821 Hom.: 103

Bravo AF: 0.126

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.61
DANN	Benign	0.24

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: rs6005879; hg19: chr22-29178314;