2-190534287-T-G

Variant names:

• chr2-190534287-T-G
• rs12622496
• NM_001142645.2:c.97+272A>C

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001142645.2(NEMP2):​c.97+272A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000135 in 1,163,592 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00017 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00013 (0 hom.)
• Consequence: NEMP2 NM_001142645.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.470
• Publications: 5 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NEMP2	NM_001142645.2	c.97+272A>C		intron_variant	Intron 1 of 8	ENST00000409150.8	NP_001136117.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NEMP2	ENST00000409150.8	c.97+272A>C		intron_variant	Intron 1 of 8	2	NM_001142645.2	ENSP00000386292.3

Frequencies

GnomAD3 genomes AF: 0.000171 AC: 26 AN: 152128 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00423

Gnomad SAS AF: 0.000207

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000294

Gnomad OTH AF: 0.00

GnomAD4 exome AF: 0.000130 AC: 131 AN: 1011346 Hom.: 0 Cov.: 19 AF XY: 0.000122 AC XY: 58 AN XY: 475640

African (AFR) AF: 0.00 AC: 0 AN: 20734

American (AMR) AF: 0.00 AC: 0 AN: 6296

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11616

East Asian (EAS) AF: 0.00550 AC: 110 AN: 20016

South Asian (SAS) AF: 0.000319 AC: 6 AN: 18786

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 16838

Middle Eastern (MID) AF: 0.000388 AC: 1 AN: 2578

European-Non Finnish (NFE) AF: 0.00000228 AC: 2 AN: 875286

Other (OTH) AF: 0.000306 AC: 12 AN: 39196

GnomAD4 genome AF: 0.000171 AC: 26 AN: 152246 Hom.: 0 Cov.: 33 AF XY: 0.000202 AC XY: 15 AN XY: 74426

African (AFR) AF: 0.00 AC: 0 AN: 41554

American (AMR) AF: 0.0000653 AC: 1 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3472

East Asian (EAS) AF: 0.00424 AC: 22 AN: 5184

South Asian (SAS) AF: 0.000207 AC: 1 AN: 4830

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10588

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0000294 AC: 2 AN: 67994

Other (OTH) AF: 0.00 AC: 0 AN: 2114

Alfa AF: 0.00 Hom.: 2056

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	0.93
DANN	Benign	0.53
PhyloP100		-0.47
PromoterAI		0.024	Neutral

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs12622496; hg19: chr2-191399013;