NM_007045.4:c.579+3427T>A

Variant names:

• chr6-167016994-T-A
• rs151606
• NM_007045.4:c.579+3427T>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_007045.4(CEP43):​c.579+3427T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.811 in 149,316 control chromosomes in the GnomAD database, including 49,138 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 0.81 (49138 hom., cov: 28)
• Consequence: CEP43 NM_007045.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.964
• Publications: 4 publications found

Genes affected

CEP43 (HGNC:17012): (centrosomal protein 43) This gene encodes a largely hydrophilic centrosomal protein that is required for anchoring microtubules to subcellular structures. A t(6;8)(q27;p11) chromosomal translocation, fusing this gene and the fibroblast growth factor receptor 1 (FGFR1) gene, has been found in cases of myeloproliferative disorder. The resulting chimeric protein contains the N-terminal leucine-rich region of this encoded protein fused to the catalytic domain of FGFR1. Alterations in this gene may also be associated with Crohn's disease, Graves' disease, and vitiligo. Alternatively spliced transcript variants that encode different proteins have been identified. [provided by RefSeq, Jul 2013]

ENSG00000272980 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007045.4. 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
	CEP43	NM_007045.4	MANE Select	c.579+3427T>A		intron	N/A	NP_008976.1
	CEP43	NM_194429.3		c.520-5415T>A		intron	N/A	NP_919410.1
	CEP43	NM_001278690.2		c.439-5415T>A		intron	N/A	NP_001265619.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CEP43	ENST00000366847.9	TSL:1 MANE Select	c.579+3427T>A		intron	N/A	ENSP00000355812.3
	ENSG00000272980	ENST00000705249.1		c.520-5415T>A		intron	N/A	ENSP00000516101.1
	CEP43	ENST00000349556.5	TSL:1	c.520-5415T>A		intron	N/A	ENSP00000230248.6

Frequencies

GnomAD3 genomes AF: 0.811 AC: 121074 AN: 149218 Hom.: 49102 Cov.: 28

Gnomad AFR AF: 0.752

Gnomad AMI AF: 0.845

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.772

Gnomad MID AF: 0.831

Gnomad NFE AF: 0.821

Gnomad OTH AF: 0.822

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.811 AC: 121155 AN: 149316 Hom.: 49138 Cov.: 28 AF XY: 0.812 AC XY: 59259 AN XY: 72980

African (AFR) AF: 0.753 AC: 30350 AN: 40330

American (AMR) AF: 0.868 AC: 13095 AN: 15094

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2960 AN: 3452

East Asian (EAS) AF: 0.986 AC: 5059 AN: 5130

South Asian (SAS) AF: 0.836 AC: 3988 AN: 4768

European-Finnish (FIN) AF: 0.772 AC: 7517 AN: 9732

Middle Eastern (MID) AF: 0.825 AC: 241 AN: 292

European-Non Finnish (NFE) AF: 0.821 AC: 55472 AN: 67540

Other (OTH) AF: 0.824 AC: 1704 AN: 2068

Alfa AF: 0.811 Hom.: 4996

Asia WGS AF: 0.889 AC: 3047 AN: 3426

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.34
DANN	Benign	0.18
PhyloP100		-0.96
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: rs151606; hg19: chr6-167430482;