17-82209113-G-T

Variant names:

• chr17-82209113-G-T
• rs4247357
• NM_001394669.1:c.-9+3672C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 19 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
CCDC57	NM_001394669.1	c.-9+3672C>A		intron_variant	Intron 1 of 18	ENST00000694881.1	NP_001381598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC57	ENST00000694881.1	c.-9+3672C>A		intron_variant	Intron 1 of 18		NM_001394669.1	ENSP00000511565.1

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

African (AFR) AF: 0.445 AC: 18409 AN: 41402

American (AMR) AF: 0.578 AC: 8813 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.590 AC: 2042 AN: 3462

East Asian (EAS) AF: 0.881 AC: 4562 AN: 5180

South Asian (SAS) AF: 0.548 AC: 2642 AN: 4818

European-Finnish (FIN) AF: 0.452 AC: 4757 AN: 10532

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.417 AC: 28312 AN: 67934

Other (OTH) AF: 0.484 AC: 1022 AN: 2112

Alfa AF: 0.436 Hom.: 7420

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
PhyloP100		0.054
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4247357; hg19: chr17-80166989;