rs1712790

Positions:

• chr11-114750747-T-C

Variant summary

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

The XM_017017211.2(NXPE2):​c.1144+44751T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 152,072 control chromosomes in the GnomAD database, including 15,547 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 (15547 hom., cov: 32)
• Consequence: NXPE2 XM_017017211.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160

Genes affected

NXPE2 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.577 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NXPE2	XM_017017211.2	c.1144+44751T>C		intron_variant			XP_016872700.1
NXPE2	XM_017017212.2	c.1144+44751T>C		intron_variant			XP_016872701.1
NXPE2	XR_001747769.2	n.1277+10991T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65072 AN: 151954 Hom.: 15551 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.459

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.510

Gnomad SAS AF: 0.594

Gnomad FIN AF: 0.550

Gnomad MID AF: 0.567

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.459

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

GnomAD4 genome AF: 0.428 AC: 65086 AN: 152072 Hom.: 15547 Cov.: 32 AF XY: 0.434 AC XY: 32280 AN XY: 74336

Gnomad4 AFR AF: 0.206

Gnomad4 AMR AF: 0.459

Gnomad4 ASJ AF: 0.516

Gnomad4 EAS AF: 0.509

Gnomad4 SAS AF: 0.595

Gnomad4 FIN AF: 0.550

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.460

Alfa AF: 0.507 Hom.: 41888

Bravo AF: 0.408

Asia WGS AF: 0.539 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.90

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1712790; hg19: chr11-114621469;