rs1127678

chr17-82101611-C-T

Variant summary

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

The NM_001394669.1(CCDC57):c.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,273,680 control chromosomes in the GnomAD database, including 29,503 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 0.23 (4212 hom., cov: 34)
  • Exomes 𝑓: 0.21 (25291 hom.)
• Consequence: CCDC57 NM_001394669.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200

Genes affected

CCDC57 (HGNC:27564): (coiled-coil domain containing 57) Involved in several processes, including G2/M transition of mitotic cell cycle; cilium assembly; and microtubule cytoskeleton organization. Located in centriolar satellite; centriole; and spindle microtubule. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC57	NM_001394669.1	c.*71G>A		3_prime_UTR_variant	19/19	ENST00000694881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC57	ENST00000694881.1	c.*71G>A		3_prime_UTR_variant	19/19		NM_001394669.1	A2

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34748 AN: 152072 Hom.: 4211 Cov.: 34

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.206 AC: 230513 AN: 1121490 Hom.: 25291 Cov.: 15 AF XY: 0.204 AC XY: 115776 AN XY: 566294

Gnomad4 AFR exome AF: 0.287

Gnomad4 AMR exome AF: 0.117

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.0545

Gnomad4 SAS exome AF: 0.161

Gnomad4 FIN exome AF: 0.217

Gnomad4 NFE exome AF: 0.219

Gnomad4 OTH exome AF: 0.195

GnomAD4 genome AF: 0.228 AC: 34763 AN: 152190 Hom.: 4212 Cov.: 34 AF XY: 0.224 AC XY: 16633 AN XY: 74392

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.165

Gnomad4 ASJ AF: 0.147

Gnomad4 EAS AF: 0.0496

Gnomad4 SAS AF: 0.151

Gnomad4 FIN AF: 0.217

Gnomad4 NFE AF: 0.229

Gnomad4 OTH AF: 0.212

Alfa AF: 0.223 Hom.: 3997

Bravo AF: 0.225

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	2.3
Dann	Benign	0.50
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1127678; hg19: chr17-80059487; COSMIC: COSV60761460; COSMIC: COSV60761460;