rs17569034

Positions:

• chr2-117917761-A-G

Variant summary

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

The NM_019044.5(CCDC93):​c.*2582T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.053 in 152,308 control chromosomes in the GnomAD database, including 287 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 0.053 (287 hom., cov: 32)
  • Exomes 𝑓: 0.10 (0 hom.)
• Consequence: CCDC93 NM_019044.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.234

Genes affected

CCDC93 (HGNC:25611): (coiled-coil domain containing 93) Involved in Golgi to plasma membrane transport and endocytic recycling. Located in intracellular membrane-bounded organelle. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000290590 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0809 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC93	NM_019044.5	c.*2582T>C		3_prime_UTR_variant	24/24	ENST00000376300.7	NP_061917.3
CCDC93	XM_011511359.2	c.*2582T>C		3_prime_UTR_variant	24/24		XP_011509661.2
CCDC93	XM_011511361.1	c.*2582T>C		3_prime_UTR_variant	23/23		XP_011509663.1
CCDC93	XM_047444816.1	c.*2582T>C		3_prime_UTR_variant	21/21		XP_047300772.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC93	ENST00000376300	c.*2582T>C		3_prime_UTR_variant	24/24	1	NM_019044.5	ENSP00000365477.2
ENSG00000290590	ENST00000434708.1	n.183-2361A>G		intron_variant		1
CCDC93	ENST00000319432	c.*2582T>C		3_prime_UTR_variant	24/24	5		ENSP00000324135.5

Frequencies

GnomAD3 genomes AF: 0.0531 AC: 8076 AN: 152142 Hom.: 288 Cov.: 32

Gnomad AFR AF: 0.0129

Gnomad AMI AF: 0.0669

Gnomad AMR AF: 0.0352

Gnomad ASJ AF: 0.0568

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0549

Gnomad FIN AF: 0.0694

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0827

Gnomad OTH AF: 0.0468

GnomAD4 exome AF: 0.104 AC: 5 AN: 48 Hom.: 0 Cov.: 0 AF XY: 0.118 AC XY: 4 AN XY: 34

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.0833

Gnomad4 NFE exome AF: 0.0769

Gnomad4 OTH exome AF: 0.333

GnomAD4 genome AF: 0.0530 AC: 8069 AN: 152260 Hom.: 287 Cov.: 32 AF XY: 0.0515 AC XY: 3837 AN XY: 74458

Gnomad4 AFR AF: 0.0129

Gnomad4 AMR AF: 0.0351

Gnomad4 ASJ AF: 0.0568

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0547

Gnomad4 FIN AF: 0.0694

Gnomad4 NFE AF: 0.0827

Gnomad4 OTH AF: 0.0464

Alfa AF: 0.0743 Hom.: 415

Bravo AF: 0.0482

Asia WGS AF: 0.0250 AC: 88 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.3
DANN	Benign	0.63
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.2

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: rs17569034; hg19: chr2-118675337;