11-114479118-C-T

Position:

• chr11-114479118-C-T

Variant summary

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

The XM_017017209.2(NXPE2):​c.-483+12169C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.614 in 152,102 control chromosomes in the GnomAD database, including 30,304 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 0.61 (30304 hom., cov: 32)
• Consequence: NXPE2 XM_017017209.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.710

Genes affected

NXPE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.834 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE2	XM_017017209.2	c.-483+12169C>T		intron_variant			XP_016872698.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.614 AC: 93257 AN: 151984 Hom.: 30250 Cov.: 32

Gnomad AFR AF: 0.841

Gnomad AMI AF: 0.397

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.607

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.512

Gnomad OTH AF: 0.597

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

GnomAD4 genome AF: 0.614 AC: 93368 AN: 152102 Hom.: 30304 Cov.: 32 AF XY: 0.612 AC XY: 45483 AN XY: 74346

Gnomad4 AFR AF: 0.841

Gnomad4 AMR AF: 0.572

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.607

Gnomad4 SAS AF: 0.569

Gnomad4 FIN AF: 0.488

Gnomad4 NFE AF: 0.512

Gnomad4 OTH AF: 0.596

Alfa AF: 0.536 Hom.: 12873

Bravo AF: 0.629

Asia WGS AF: 0.594 AC: 2067 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs581015; hg19: chr11-114349840;