2-190520198-G-A

Variant names:

• chr2-190520198-G-A
• rs13019278
• NM_001142645.2:c.214-1015C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001142645.2. 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
	NEMP2	NM_001142645.2	MANE Select	c.214-1015C>T		intron	N/A	NP_001136117.1
	NEMP2	NR_136298.2		n.281-1015C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NEMP2	ENST00000409150.8	TSL:2 MANE Select	c.214-1015C>T		intron	N/A	ENSP00000386292.3
	NEMP2	ENST00000421038.1	TSL:3	c.7-1015C>T		intron	N/A	ENSP00000410306.1
	NEMP2	ENST00000343105.9	TSL:4	n.214-1176C>T		intron	N/A	ENSP00000340087.5

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

African (AFR) AF: 0.269 AC: 11155 AN: 41396

American (AMR) AF: 0.460 AC: 7016 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1017 AN: 3470

East Asian (EAS) AF: 0.464 AC: 2400 AN: 5172

South Asian (SAS) AF: 0.222 AC: 1068 AN: 4816

European-Finnish (FIN) AF: 0.427 AC: 4514 AN: 10560

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.255 AC: 17300 AN: 67944

Other (OTH) AF: 0.280 AC: 590 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.28
DANN	Benign	0.39
PhyloP100		-1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs13019278; hg19: chr2-191384924;