rs13019278

chr2-190520198-G-Achr2-190520198-G-Cchr2-190520198-G-T

Variant summary

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

The NM_001142645.2(NEMP2):c.214-1015C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 151,942 control chromosomes in the GnomAD database, including 7,515 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 0.30 (7515 hom., cov: 32)
• Consequence: NEMP2 NM_001142645.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.26

Genes affected

NEMP2 (HGNC:33700): (nuclear envelope integral membrane protein 2) Predicted to be located in nuclear inner membrane. Predicted to be integral component of membrane. Predicted to be active in nuclear envelope. [provided by Alliance of Genome Resources, Apr 2022]

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 = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NEMP2	NM_001142645.2	c.214-1015C>T		intron_variant		ENST00000409150.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NEMP2	ENST00000409150.8	c.214-1015C>T		intron_variant		2	NM_001142645.2	P1

Frequencies

GnomAD3 genomes AF: 0.298 AC: 45293 AN: 151822 Hom.: 7499 Cov.: 32

Gnomad AFR AF: 0.270

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.427

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.298 AC: 45336 AN: 151942 Hom.: 7515 Cov.: 32 AF XY: 0.311 AC XY: 23097 AN XY: 74282

Gnomad4 AFR AF: 0.269

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.464

Gnomad4 SAS AF: 0.222

Gnomad4 FIN AF: 0.427

Gnomad4 NFE AF: 0.255

Gnomad4 OTH AF: 0.280

Alfa AF: 0.283 Hom.: 840

Bravo AF: 0.308

Asia WGS AF: 0.329 AC: 1147 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	0.28
Dann	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs13019278; hg19: chr2-191384924;