11-114516108-C-T

Position:

• chr11-114516108-C-T

Variant summary

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

The XM_017017207.2(NXPE2):​c.-639-1448C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.349 in 152,038 control chromosomes in the GnomAD database, including 9,587 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 0.35 (9587 hom., cov: 32)
• Consequence: NXPE2 XM_017017207.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.438

Genes affected

NXPE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.637 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE2	XM_017017207.2	c.-639-1448C>T		intron_variant			XP_016872696.1
NXPE2	XM_017017209.2	c.-482-10515C>T		intron_variant			XP_016872698.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.349 AC: 53032 AN: 151920 Hom.: 9572 Cov.: 32

Gnomad AFR AF: 0.315

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.328

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.656

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.349 AC: 53083 AN: 152038 Hom.: 9587 Cov.: 32 AF XY: 0.353 AC XY: 26230 AN XY: 74294

Gnomad4 AFR AF: 0.315

Gnomad4 AMR AF: 0.328

Gnomad4 ASJ AF: 0.351

Gnomad4 EAS AF: 0.655

Gnomad4 SAS AF: 0.330

Gnomad4 FIN AF: 0.399

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.340

Alfa AF: 0.347 Hom.: 2174

Bravo AF: 0.344

Asia WGS AF: 0.469 AC: 1634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.2
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs561722; hg19: chr11-114386830;