rs730532

Positions:

• chr14-52052093-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NID2	NM_007361.4	c.1429+1486C>T		intron_variant		ENST00000216286.10	NP_031387.3
NID2	XM_005267405.5	c.1510+1486C>T		intron_variant			XP_005267462.1
NID2	XM_005267406.5	c.1510+1486C>T		intron_variant			XP_005267463.1
NID2	XM_005267407.5	c.1429+1486C>T		intron_variant			XP_005267464.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NID2	ENST00000216286.10	c.1429+1486C>T		intron_variant		1	NM_007361.4	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

Gnomad4 AFR AF: 0.548

Gnomad4 AMR AF: 0.577

Gnomad4 ASJ AF: 0.686

Gnomad4 EAS AF: 0.494

Gnomad4 SAS AF: 0.717

Gnomad4 FIN AF: 0.756

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.674

Alfa AF: 0.748 Hom.: 50504

Bravo AF: 0.656

Asia WGS AF: 0.601 AC: 2088 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.79

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: rs730532; hg19: chr14-52518811;