4-67470861-A-T

Position:

• chr4-67470861-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001812.4(CENPC):​c.*1744T>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 0.626 in 151,988 control chromosomes in the GnomAD database, including 30,023 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 0.63 (30017 hom., cov: 32)
  • Exomes 𝑓: 0.62 (6 hom.)
• Consequence: CENPC NM_001812.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.874

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CENPC	NM_001812.4	c.*1744T>A		3_prime_UTR_variant	19/19	ENST00000273853.11
CENPC	NM_001362481.2	c.*1744T>A		3_prime_UTR_variant	19/19
CENPC	XM_047449526.1	c.*1752T>A		3_prime_UTR_variant	18/18
CENPC	NR_155754.2	n.4842T>A		non_coding_transcript_exon_variant	19/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CENPC	ENST00000273853.11	c.*1744T>A		3_prime_UTR_variant	19/19	1	NM_001812.4	P1

Frequencies

GnomAD3 genomes AF: 0.626 AC: 95059 AN: 151844 Hom.: 29976 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.554

Gnomad AMR AF: 0.732

Gnomad ASJ AF: 0.633

Gnomad EAS AF: 0.812

Gnomad SAS AF: 0.696

Gnomad FIN AF: 0.568

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.664

GnomAD4 exome AF: 0.615 AC: 16 AN: 26 Hom.: 6 Cov.: 0 AF XY: 0.611 AC XY: 11 AN XY: 18

Gnomad4 FIN exome AF: 0.250

Gnomad4 NFE exome AF: 0.611

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.626 AC: 95148 AN: 151962 Hom.: 30017 Cov.: 32 AF XY: 0.631 AC XY: 46831 AN XY: 74226

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.732

Gnomad4 ASJ AF: 0.633

Gnomad4 EAS AF: 0.812

Gnomad4 SAS AF: 0.697

Gnomad4 FIN AF: 0.568

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.667

Alfa AF: 0.601 Hom.: 3402

Bravo AF: 0.640

Asia WGS AF: 0.768 AC: 2670 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.0
DANN	Benign	0.71

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: rs9312181; hg19: chr4-68336579;