rs1127678

Variant names:

• chr17-82101611-C-G
• rs1127678
• NM_001394669.1:c.*71G>C

Your query was ambiguous. Multiple possible variants found:

• chr17-82101611-C-G
• chr17-82101611-C-T

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.*71G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000116 in 1,123,942 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 34)
  • Exomes 𝑓: 0.000012 (0 hom.)
• Consequence: CCDC57 NM_001394669.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• Publications: 0 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.*71G>C		3_prime_UTR	Exon 19 of 19	NP_001381598.1
	CCDC57	NM_001394670.1		c.*71G>C		3_prime_UTR	Exon 20 of 20	NP_001381599.1
	CCDC57	NM_198082.4		c.*71G>C		3_prime_UTR	Exon 17 of 17	NP_932348.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CCDC57	ENST00000694881.1	MANE Select	c.*71G>C		3_prime_UTR	Exon 19 of 19	ENSP00000511565.1
	CCDC57	ENST00000665763.1		c.*71G>C		3_prime_UTR	Exon 20 of 20	ENSP00000499556.1
	CCDC57	ENST00000875325.1		c.*71G>C		3_prime_UTR	Exon 20 of 20	ENSP00000545384.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 0.0000116 AC: 13 AN: 1123942 Hom.: 0 Cov.: 15 AF XY: 0.0000106 AC XY: 6 AN XY: 567466

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.0000809 AC: 2 AN: 24722

American (AMR) AF: 0.00 AC: 0 AN: 29998

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 21936

East Asian (EAS) AF: 0.00 AC: 0 AN: 36722

South Asian (SAS) AF: 0.00 AC: 0 AN: 70776

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44496

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4796

European-Non Finnish (NFE) AF: 0.0000131 AC: 11 AN: 841458

Other (OTH) AF: 0.00 AC: 0 AN: 49038

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.49
PhyloP100		-0.20
PromoterAI		-0.095	Neutral

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: rs1127678; hg19: chr17-80059487;