ENST00000651326.1:n.2417+40815G>A

Variant names:

• chr6-126431652-C-T
• rs4565329
• ENST00000651326.1:n.2417+40815G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000651326.1(ENSG00000293110):​n.2417+40815G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.431 in 152,006 control chromosomes in the GnomAD database, including 16,478 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 0.43 (16478 hom., cov: 31)
• Consequence: ENSG00000293110 ENST00000651326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 23 publications found

Genes affected

ENSG00000293110 (HGNC:):

CENPW (HGNC:21488): (centromere protein W) Predicted to enable DNA binding activity and protein heterodimerization activity. Involved in chromosome segregation; kinetochore assembly; and mitotic cell cycle. Located in kinetochore and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000651326.1. 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
	CENPW	NR_104462.2		n.400-1899C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293110	ENST00000651326.1		n.2417+40815G>A		intron	N/A
	ENSG00000293110	ENST00000652383.1		n.630+100011G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65574 AN: 151888 Hom.: 16477 Cov.: 31

Gnomad AFR AF: 0.211

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.610

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.676

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.472

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

GnomAD4 genome AF: 0.431 AC: 65577 AN: 152006 Hom.: 16478 Cov.: 31 AF XY: 0.442 AC XY: 32793 AN XY: 74272

African (AFR) AF: 0.211 AC: 8741 AN: 41492

American (AMR) AF: 0.611 AC: 9319 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1657 AN: 3466

East Asian (EAS) AF: 0.974 AC: 5035 AN: 5168

South Asian (SAS) AF: 0.676 AC: 3260 AN: 4820

European-Finnish (FIN) AF: 0.435 AC: 4579 AN: 10534

Middle Eastern (MID) AF: 0.656 AC: 193 AN: 294

European-Non Finnish (NFE) AF: 0.462 AC: 31401 AN: 67942

Other (OTH) AF: 0.467 AC: 987 AN: 2114

Alfa AF: 0.424 Hom.: 3008

Bravo AF: 0.437

Asia WGS AF: 0.693 AC: 2407 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	1.8
DANN	Benign	0.68
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs4565329; hg19: chr6-126752798;