rs7949181

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NXPE2	XM_017017211.2	c.1145-10392T>C		intron_variant	Intron 5 of 5		XP_016872700.1
NXPE2	XM_017017212.2	c.1145-10392T>C		intron_variant	Intron 5 of 6		XP_016872701.1
NXPE2	XR_001747769.2	n.1278-10392T>C		intron_variant	Intron 6 of 6
LOC105369506	XR_948042.3	n.87-11944A>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000297869	ENST00000751459.1	n.193-11944A>G		intron_variant	Intron 2 of 3
ENSG00000297869	ENST00000751460.1	n.215-11944A>G		intron_variant	Intron 2 of 3
ENSG00000297869	ENST00000751461.1	n.249+2963A>G		intron_variant	Intron 1 of 3

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 v4.3

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;