17-82101456-A-C

Position:

• chr17-82101456-A-C

Variant summary

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

The 17-82101456-A-C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 497,564 control chromosomes in the GnomAD database, including 70,177 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 0.55 (23679 hom., cov: 33)
  • Exomes 𝑓: 0.50 (46498 hom.)
• Consequence: CCDC57 NM_001394669.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.94

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=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CCDC57	NM_001394669.1			downstream_gene_variant		ENST00000694881.1	NP_001381598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CCDC57	ENST00000694881.1			downstream_gene_variant			NM_001394669.1	ENSP00000511565	A2

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83163 AN: 152012 Hom.: 23677 Cov.: 33

Gnomad AFR AF: 0.635

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.421

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.119

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.535

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.573

Gnomad OTH AF: 0.530

GnomAD4 exome AF: 0.502 AC: 173478 AN: 345434 Hom.: 46498 Cov.: 3 AF XY: 0.498 AC XY: 89340 AN XY: 179404

Gnomad4 AFR exome AF: 0.618

Gnomad4 AMR exome AF: 0.353

Gnomad4 ASJ exome AF: 0.382

Gnomad4 EAS exome AF: 0.110

Gnomad4 SAS exome AF: 0.430

Gnomad4 FIN exome AF: 0.535

Gnomad4 NFE exome AF: 0.560

Gnomad4 OTH exome AF: 0.495

GnomAD4 genome AF: 0.547 AC: 83194 AN: 152130 Hom.: 23679 Cov.: 33 AF XY: 0.539 AC XY: 40126 AN XY: 74378

Gnomad4 AFR AF: 0.634

Gnomad4 AMR AF: 0.420

Gnomad4 ASJ AF: 0.396

Gnomad4 EAS AF: 0.119

Gnomad4 SAS AF: 0.431

Gnomad4 FIN AF: 0.535

Gnomad4 NFE AF: 0.573

Gnomad4 OTH AF: 0.525

Alfa AF: 0.543 Hom.: 8630

Bravo AF: 0.537

Asia WGS AF: 0.287 AC: 1000 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6502051; hg19: chr17-80059332;