chr3-101727363-AAT-A

Position:

• chr3-101727363-AAT-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_024548.4(CEP97):​c.187-17_187-16delAT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.336 in 1,591,590 control chromosomes in the GnomAD database, including 92,109 homozygotes. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.31 (7725 hom., cov: 0)
  • Exomes 𝑓: 0.34 (84384 hom.)
• Consequence: CEP97 NM_024548.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.888

Genes affected

CEP97 (HGNC:26244): (centrosomal protein 97) Predicted to enable calmodulin binding activity. Involved in negative regulation of cilium assembly and regulation of mitotic spindle assembly. Located in centriolar satellite and cytosol. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]

CEP97 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 3-101727363-AAT-A is Benign according to our data. Variant chr3-101727363-AAT-A is described in ClinVar as [Benign]. Clinvar id is 1575560.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.342 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP97	NM_024548.4	c.187-17_187-16delAT		intron_variant		ENST00000341893.8	NP_078824.2
CEP97	NM_001410784.1	c.187-17_187-16delAT		intron_variant			NP_001397713.1
CEP97	NM_001303401.2	c.187-17_187-16delAT		intron_variant			NP_001290330.1
CEP97	NM_001410785.1	c.187-17_187-16delAT		intron_variant			NP_001397714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP97	ENST00000341893.8	c.187-17_187-16delAT		intron_variant		1	NM_024548.4	ENSP00000342510.3

Frequencies

GnomAD3 genomes AF: 0.315 AC: 47840 AN: 151854 Hom.: 7731 Cov.: 0

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.213

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.304

GnomAD3 exomes AF: 0.309 AC: 74548 AN: 241548 Hom.: 12025 AF XY: 0.308 AC XY: 40185 AN XY: 130500

Gnomad AFR exome AF: 0.274

Gnomad AMR exome AF: 0.233

Gnomad ASJ exome AF: 0.354

Gnomad EAS exome AF: 0.287

Gnomad SAS exome AF: 0.226

Gnomad FIN exome AF: 0.367

Gnomad NFE exome AF: 0.344

Gnomad OTH exome AF: 0.322

GnomAD4 exome AF: 0.338 AC: 486935 AN: 1439618 Hom.: 84384 AF XY: 0.335 AC XY: 239999 AN XY: 716176

Gnomad4 AFR exome AF: 0.270

Gnomad4 AMR exome AF: 0.238

Gnomad4 ASJ exome AF: 0.357

Gnomad4 EAS exome AF: 0.342

Gnomad4 SAS exome AF: 0.226

Gnomad4 FIN exome AF: 0.363

Gnomad4 NFE exome AF: 0.351

Gnomad4 OTH exome AF: 0.341

GnomAD4 genome AF: 0.315 AC: 47839 AN: 151972 Hom.: 7725 Cov.: 0 AF XY: 0.314 AC XY: 23301 AN XY: 74270

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.301

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.301

Alfa AF: 0.329 Hom.: 1551

Bravo AF: 0.309

Asia WGS AF: 0.225 AC: 779 AN: 3476

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 31, 2024

- -

Computational scores

Source: dbNSFP v4.3

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: rs3070526; hg19: chr3-101446207;