6-126446454-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000651326.1(ENSG00000293110):n.2417+26013G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.454 in 149,892 control chromosomes in the GnomAD database, including 17,133 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 0.45 (17133 hom., cov: 28)
• Consequence: ENST00000651326.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.49

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• 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	UniProt
CENPW	NR_104462.2	n.474+12829C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651326.1	n.2417+26013G>A		intron_variant, non_coding_transcript_variant
	ENST00000652383.1	n.630+85209G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.455 AC: 68091 AN: 149774 Hom.: 17130 Cov.: 28

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.479

Gnomad EAS AF: 0.974

Gnomad SAS AF: 0.675

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.461

Gnomad OTH AF: 0.496

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

GnomAD4 genome AF: 0.454 AC: 68118 AN: 149892 Hom.: 17133 Cov.: 28 AF XY: 0.464 AC XY: 33912 AN XY: 73130

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.621

Gnomad4 ASJ AF: 0.479

Gnomad4 EAS AF: 0.974

Gnomad4 SAS AF: 0.675

Gnomad4 FIN AF: 0.436

Gnomad4 NFE AF: 0.461

Gnomad4 OTH AF: 0.492

Alfa AF: 0.486 Hom.: 22964

Bravo AF: 0.465

Asia WGS AF: 0.706 AC: 2446 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
Cadd	Benign	19
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1361108; hg19: chr6-126767600;