17-82209113-G-T

Position:

• chr17-82209113-G-T

Variant summary

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

The NM_001394669.1(CCDC57):​c.-9+3672C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 151,900 control chromosomes in the GnomAD database, including 17,405 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 0.47 (17405 hom., cov: 32)
• Consequence: CCDC57 NM_001394669.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0540

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.859 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CCDC57	NM_001394669.1	c.-9+3672C>A		intron_variant		ENST00000694881.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC57	ENST00000694881.1	c.-9+3672C>A		intron_variant			NM_001394669.1	A2

Frequencies

GnomAD3 genomes AF: 0.468 AC: 70982 AN: 151782 Hom.: 17366 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.577

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.549

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.479

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.468 AC: 71083 AN: 151900 Hom.: 17405 Cov.: 32 AF XY: 0.475 AC XY: 35261 AN XY: 74246

Gnomad4 AFR AF: 0.445

Gnomad4 AMR AF: 0.578

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.548

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.417

Gnomad4 OTH AF: 0.484

Alfa AF: 0.435 Hom.: 6564

Bravo AF: 0.483

Asia WGS AF: 0.708 AC: 2460 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.7
DANN	Benign	0.87

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: rs4247357; hg19: chr17-80166989;