chr11-114794390-T-C

Variant names:

• chr11-114794390-T-C
• rs7949181
• ENST00000751459.1:n.193-11944A>G

Variant summary

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

The ENST00000751459.1(ENSG00000297869):​n.193-11944A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 152,094 control chromosomes in the GnomAD database, including 5,960 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 0.28 (5960 hom., cov: 32)
• Consequence: ENSG00000297869 ENST00000751459.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 3 publications found

Genes affected

ENSG00000297869 (HGNC:):

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.346 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751459.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297869	ENST00000751459.1		n.193-11944A>G		intron	N/A
	ENSG00000297869	ENST00000751460.1		n.215-11944A>G		intron	N/A
	ENSG00000297869	ENST00000751461.1		n.249+2963A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41942 AN: 151976 Hom.: 5933 Cov.: 32

Gnomad AFR AF: 0.323

Gnomad AMI AF: 0.306

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.232

Gnomad SAS AF: 0.334

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.236

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.276 AC: 42021 AN: 152094 Hom.: 5960 Cov.: 32 AF XY: 0.281 AC XY: 20882 AN XY: 74338

African (AFR) AF: 0.323 AC: 13401 AN: 41464

American (AMR) AF: 0.354 AC: 5408 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3468

East Asian (EAS) AF: 0.232 AC: 1200 AN: 5168

South Asian (SAS) AF: 0.334 AC: 1606 AN: 4810

European-Finnish (FIN) AF: 0.259 AC: 2739 AN: 10590

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.236 AC: 16043 AN: 68002

Other (OTH) AF: 0.271 AC: 572 AN: 2110

Alfa AF: 0.251 Hom.: 8029

Bravo AF: 0.283

Asia WGS AF: 0.317 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.31
DANN	Benign	0.47
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs7949181; hg19: chr11-114665112;