chr17-82101611-C-T

Variant names:

• chr17-82101611-C-T
• rs1127678
• NM_001394669.1:c.*71G>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.*71G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.208 in 1,273,680 control chromosomes in the GnomAD database, including 29,503 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 0.23 (4212 hom., cov: 34)
  • Exomes 𝑓: 0.21 (25291 hom.)
• Consequence: CCDC57 NM_001394669.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.200
• 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC57	NM_001394669.1	c.*71G>A		3_prime_UTR_variant	Exon 19 of 19	ENST00000694881.1	NP_001381598.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC57	ENST00000694881.1	c.*71G>A		3_prime_UTR_variant	Exon 19 of 19		NM_001394669.1	ENSP00000511565.1

Frequencies

GnomAD3 genomes AF: 0.228 AC: 34748 AN: 152072 Hom.: 4211 Cov.: 34

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.146

Gnomad AMR AF: 0.165

Gnomad ASJ AF: 0.147

Gnomad EAS AF: 0.0497

Gnomad SAS AF: 0.152

Gnomad FIN AF: 0.217

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.229

Gnomad OTH AF: 0.214

GnomAD4 exome AF: 0.206 AC: 230513 AN: 1121490 Hom.: 25291 Cov.: 15 AF XY: 0.204 AC XY: 115776 AN XY: 566294

African (AFR) AF: 0.287 AC: 7083 AN: 24676

American (AMR) AF: 0.117 AC: 3503 AN: 29978

Ashkenazi Jewish (ASJ) AF: 0.136 AC: 2978 AN: 21916

East Asian (EAS) AF: 0.0545 AC: 1999 AN: 36696

South Asian (SAS) AF: 0.161 AC: 11351 AN: 70676

European-Finnish (FIN) AF: 0.217 AC: 9630 AN: 44452

Middle Eastern (MID) AF: 0.185 AC: 887 AN: 4786

European-Non Finnish (NFE) AF: 0.219 AC: 183544 AN: 839338

Other (OTH) AF: 0.195 AC: 9538 AN: 48972

GnomAD4 genome AF: 0.228 AC: 34763 AN: 152190 Hom.: 4212 Cov.: 34 AF XY: 0.224 AC XY: 16633 AN XY: 74392

African (AFR) AF: 0.295 AC: 12229 AN: 41520

American (AMR) AF: 0.165 AC: 2519 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.147 AC: 511 AN: 3468

East Asian (EAS) AF: 0.0496 AC: 257 AN: 5178

South Asian (SAS) AF: 0.151 AC: 730 AN: 4830

European-Finnish (FIN) AF: 0.217 AC: 2295 AN: 10600

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.229 AC: 15591 AN: 67970

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.224 Hom.: 6053

Bravo AF: 0.225

Asia WGS AF: 0.109 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.50
PhyloP100		-0.20
PromoterAI		-0.052	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
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: rs1127678; hg19: chr17-80059487; COSMIC: COSV60761460; COSMIC: COSV60761460;