14-52052093-G-A

Variant names:

• chr14-52052093-G-A
• rs730532
• NM_007361.4:c.1429+1486C>T

Variant summary

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

The NM_007361.4(NID2):​c.1429+1486C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,110 control chromosomes in the GnomAD database, including 36,028 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 0.68 (36028 hom., cov: 32)
• Consequence: NID2 NM_007361.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.153
• Publications: 13 publications found

Genes affected

NID2 (HGNC:13389): (nidogen 2) This gene encodes a member of the nidogen family of basement membrane proteins. This protein is a cell-adhesion protein that binds collagens I and IV and laminin and may be involved in maintaining the structure of the basement membrane.[provided by RefSeq, Jun 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.774 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007361.4. 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
	NID2	NM_007361.4	MANE Select	c.1429+1486C>T		intron	N/A	NP_031387.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NID2	ENST00000216286.10	TSL:1 MANE Select	c.1429+1486C>T		intron	N/A	ENSP00000216286.4

Frequencies

GnomAD3 genomes AF: 0.680 AC: 103300 AN: 151992 Hom.: 36030 Cov.: 32

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.578

Gnomad ASJ AF: 0.686

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.717

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.677

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.679 AC: 103327 AN: 152110 Hom.: 36028 Cov.: 32 AF XY: 0.675 AC XY: 50152 AN XY: 74354

African (AFR) AF: 0.548 AC: 22745 AN: 41476

American (AMR) AF: 0.577 AC: 8810 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.686 AC: 2383 AN: 3472

East Asian (EAS) AF: 0.494 AC: 2546 AN: 5158

South Asian (SAS) AF: 0.717 AC: 3452 AN: 4816

European-Finnish (FIN) AF: 0.756 AC: 8001 AN: 10586

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53016 AN: 68012

Other (OTH) AF: 0.674 AC: 1419 AN: 2106

Alfa AF: 0.727 Hom.: 82417

Bravo AF: 0.656

Asia WGS AF: 0.601 AC: 2088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.15
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: rs730532; hg19: chr14-52518811;