6-126377573-A-G

Position:

• chr6-126377573-A-G

Variant summary

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

The NR_104462.2(CENPW):​n.399+31255A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.43 in 152,012 control chromosomes in the GnomAD database, including 16,394 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 (16394 hom., cov: 32)
• Consequence: CENPW NR_104462.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545

Genes affected

ENSG00000286215 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.952 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CENPW	NR_104462.2	n.399+31255A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000286215	ENST00000651326.1	n.2418-70874T>C		intron_variant
ENSG00000286215	ENST00000652383.1	n.631-66816T>C		intron_variant

Frequencies

GnomAD3 genomes AF: 0.430 AC: 65338 AN: 151894 Hom.: 16393 Cov.: 32

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.442

Gnomad AMR AF: 0.609

Gnomad ASJ AF: 0.486

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.434

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.474

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

GnomAD4 genome AF: 0.430 AC: 65340 AN: 152012 Hom.: 16394 Cov.: 32 AF XY: 0.440 AC XY: 32692 AN XY: 74308

Gnomad4 AFR AF: 0.209

Gnomad4 AMR AF: 0.609

Gnomad4 ASJ AF: 0.486

Gnomad4 EAS AF: 0.975

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.434

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.468

Alfa AF: 0.484 Hom.: 40865

Bravo AF: 0.436

Asia WGS AF: 0.695 AC: 2411 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
CADD	Benign	1.7
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9388489; hg19: chr6-126698719; COSMIC: COSV69424649;