4-67492096-A-T

Variant names:

• chr4-67492096-A-T
• rs1497430
• NM_001812.4:c.2515+84T>A

Variant summary

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

The NM_001812.4(CENPC):​c.2515+84T>A 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: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CENPC NM_001812.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.68
• Publications: 4 publications found

Genes affected

CENPC (HGNC:1854): (centromere protein C) Centromere protein C 1 is a centromere autoantigen and a component of the inner kinetochore plate. The protein is required for maintaining proper kinetochore size and a timely transition to anaphase. A putative pseudogene exists on chromosome 12. [provided by RefSeq, Jul 2008]

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=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001812.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPC	NM_001812.4	MANE Select	c.2515+84T>A		intron	N/A	NP_001803.2
	CENPC	NM_001362481.2		c.2491+84T>A		intron	N/A	NP_001349410.1
	CENPC	NR_155754.2		n.2781+84T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CENPC	ENST00000273853.11	TSL:1 MANE Select	c.2515+84T>A		intron	N/A	ENSP00000273853.6
	CENPC	ENST00000506882.5	TSL:1	n.*1239+84T>A		intron	N/A	ENSP00000426078.1
	CENPC	ENST00000515140.1	TSL:1	n.*167+84T>A		intron	N/A	ENSP00000425255.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 736872 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 378518

African (AFR) AF: 0.00 AC: 0 AN: 18202

American (AMR) AF: 0.00 AC: 0 AN: 28894

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 17790

East Asian (EAS) AF: 0.00 AC: 0 AN: 31694

South Asian (SAS) AF: 0.00 AC: 0 AN: 55024

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43208

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2594

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 504364

Other (OTH) AF: 0.00 AC: 0 AN: 35102

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	7.0
DANN	Benign	0.82
PhyloP100		1.7
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs1497430; hg19: chr4-68357814;