rs6005881

Positions:

• chr22-28787145-A-G
• chr22-28787145-A-T

Variant summary

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

The NM_173510.4(CCDC117):​c.*819A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,292 control chromosomes in the GnomAD database, including 16,087 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 (16066 hom., cov: 31)
  • Exomes 𝑓: 0.37 (21 hom.)
• Consequence: CCDC117 NM_173510.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.185

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=-0.92).
• 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	Protein	UniProt
CCDC117	NM_173510.4	c.*819A>G		3_prime_UTR_variant	5/5	ENST00000249064.9	NP_775781.1
CCDC117	NM_001284263.2	c.*819A>G		3_prime_UTR_variant	4/4		NP_001271192.1
CCDC117	NM_001284264.2	c.*819A>G		3_prime_UTR_variant	4/4		NP_001271193.1
CCDC117	NM_001284265.1	c.*819A>G		3_prime_UTR_variant	5/5		NP_001271194.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC117	ENST00000249064.9	c.*819A>G		3_prime_UTR_variant	5/5	1	NM_173510.4	ENSP00000249064.4
CCDC117	ENST00000448492.6	c.*819A>G		3_prime_UTR_variant	4/4	2		ENSP00000389478.2
CCDC117	ENST00000421503.6	c.*819A>G		3_prime_UTR_variant	4/4	2		ENSP00000387827.2

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65154 AN: 151758 Hom.: 16015 Cov.: 31

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.332

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.393

GnomAD4 exome AF: 0.370 AC: 154 AN: 416 Hom.: 21 Cov.: 0 AF XY: 0.357 AC XY: 90 AN XY: 252

Gnomad4 FIN exome AF: 0.371

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.430 AC: 65270 AN: 151876 Hom.: 16066 Cov.: 31 AF XY: 0.432 AC XY: 32028 AN XY: 74216

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.332

Gnomad4 EAS AF: 0.676

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.373

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.398

Alfa AF: 0.330 Hom.: 8620

Bravo AF: 0.432

Asia WGS AF: 0.619 AC: 2152 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.39

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: rs6005881; hg19: chr22-29183133; COSMIC: COSV50771416; COSMIC: COSV50771416;