3-101727363-A-ATTT

Position:

• chr3-101727363-A-ATTT

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_024548.4(CEP97):​c.187-20_187-19insTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CEP97 NM_024548.4 intron
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0580

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 Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 3-101727363-A-ATTT is Benign according to our data. Variant chr3-101727363-A-ATTT is described in ClinVar as [Likely_benign]. Clinvar id is 2976868.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CEP97	NM_024548.4	c.187-20_187-19insTTT		intron_variant		ENST00000341893.8	NP_078824.2
CEP97	NM_001410784.1	c.187-20_187-19insTTT		intron_variant			NP_001397713.1
CEP97	NM_001303401.2	c.187-20_187-19insTTT		intron_variant			NP_001290330.1
CEP97	NM_001410785.1	c.187-20_187-19insTTT		intron_variant			NP_001397714.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CEP97	ENST00000341893.8	c.187-20_187-19insTTT		intron_variant		1	NM_024548.4	ENSP00000342510.3

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome AF: 0.00000208 AC: 3 AN: 1442806 Hom.: 0 Cov.: 0 AF XY: 0.00000279 AC XY: 2 AN XY: 717688

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000714

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 18, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-101446207;