rs1712790

Variant names:

• chr11-114750747-T-C
• rs1712790
• XM_017017211.2:c.1144+44751T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001747769.2(NXPE2):​n.1277+10991T>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 XR_001747769.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 19 publications found

Genes affected

NXPE2 (HGNC:26331): (neurexophilin and PC-esterase domain family member 2) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.206 AC: 8557 AN: 41466

American (AMR) AF: 0.459 AC: 7006 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1790 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5174

South Asian (SAS) AF: 0.595 AC: 2872 AN: 4824

European-Finnish (FIN) AF: 0.550 AC: 5805 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 161 AN: 292

European-Non Finnish (NFE) AF: 0.516 AC: 35059 AN: 67986

Other (OTH) AF: 0.460 AC: 974 AN: 2116

Alfa AF: 0.486 Hom.: 61409

Bravo AF: 0.408

Asia WGS AF: 0.539 AC: 1875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	5.1
DANN	Benign	0.90
PhyloP100		-0.016

Splicing

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

Other links and lift over

dbSNP: rs1712790; hg19: chr11-114621469;