rs2152876

Variant names:

• chr6-126440082-G-A
• rs2152876
• ENST00000651326.1:n.2417+32385C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-126440082-G-A
• chr6-126440082-G-C
• chr6-126440082-G-T

Variant summary

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

The ENST00000651326.1(ENSG00000293110):​n.2417+32385C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.455 in 151,410 control chromosomes in the GnomAD database, including 17,391 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 0.46 (17391 hom., cov: 32)
• Consequence: ENSG00000293110 ENST00000651326.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.374
• Publications: 15 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.953 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CENPW	NR_104462.2	n.474+6457G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293110	ENST00000651326.1	n.2417+32385C>T		intron_variant	Intron 6 of 6
ENSG00000293110	ENST00000652383.1	n.630+91581C>T		intron_variant	Intron 3 of 4
ENSG00000307217	ENST00000824601.1	n.77+6457G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.456 AC: 68942 AN: 151292 Hom.: 17388 Cov.: 32

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.480

Gnomad EAS AF: 0.975

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.435

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.463

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.455 AC: 68967 AN: 151410 Hom.: 17391 Cov.: 32 AF XY: 0.465 AC XY: 34386 AN XY: 73976

African (AFR) AF: 0.293 AC: 12114 AN: 41388

American (AMR) AF: 0.621 AC: 9403 AN: 15136

Ashkenazi Jewish (ASJ) AF: 0.480 AC: 1657 AN: 3450

East Asian (EAS) AF: 0.975 AC: 5020 AN: 5148

South Asian (SAS) AF: 0.678 AC: 3259 AN: 4810

European-Finnish (FIN) AF: 0.435 AC: 4589 AN: 10554

Middle Eastern (MID) AF: 0.663 AC: 195 AN: 294

European-Non Finnish (NFE) AF: 0.463 AC: 31285 AN: 67622

Other (OTH) AF: 0.495 AC: 1040 AN: 2102

Alfa AF: 0.413 Hom.: 3694

Bravo AF: 0.465

Asia WGS AF: 0.705 AC: 2440 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.17
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2152876; hg19: chr6-126761228;