chr17-82209113-G-C

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_001394669.1(CCDC57):​c.-9+3672C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001394669.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC57	NM_001394669.1	MANE Select	c.-9+3672C>G		intron	N/A	NP_001381598.1	A0A590UJT6
	CCDC57	NM_001394670.1		c.-326-1065C>G		intron	N/A	NP_001381599.1	A0A590UJT6
	CCDC57	NM_198082.4		c.-9+3672C>G		intron	N/A	NP_932348.2	Q2TAC2-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC57	ENST00000694881.1	MANE Select	c.-9+3672C>G		intron	N/A	ENSP00000511565.1	A0A590UJT6
	CCDC57	ENST00000392343.3	TSL:1	c.-326-1065C>G		intron	N/A	ENSP00000376154.3	Q2TAC2-2
	CCDC57	ENST00000665763.1		c.-210-1065C>G		intron	N/A	ENSP00000499556.1	A0A590UJT6

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.8
DANN	Benign	0.80
PhyloP100		0.054

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;