rs7153720

chr14-50813954-C-T

Variant summary

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

The NM_020921.4(NIN):c.184-7136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,992 control chromosomes in the GnomAD database, including 12,169 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 0.38 (12169 hom., cov: 33)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

Genes affected

NIN (HGNC:14906): (ninein) This gene encodes one of the proteins important for centrosomal function. This protein is important for positioning and anchoring the microtubules minus-ends in epithelial cells. Localization of this protein to the centrosome requires three leucine zippers in the central coiled-coil domain. Multiple alternatively spliced transcript variants that encode different isoforms have been reported. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIN	NM_020921.4	c.184-7136G>A		intron_variant		ENST00000530997.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIN	ENST00000530997.7	c.184-7136G>A		intron_variant		5	NM_020921.4	P2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57000 AN: 151872 Hom.: 12165 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.375 AC: 57017 AN: 151992 Hom.: 12169 Cov.: 33 AF XY: 0.371 AC XY: 27554 AN XY: 74292

Gnomad4 AFR AF: 0.189

Gnomad4 AMR AF: 0.288

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.406

Gnomad4 FIN AF: 0.442

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.383

Alfa AF: 0.475 Hom.: 22599

Bravo AF: 0.354

Asia WGS AF: 0.322 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.039
Dann	Benign	0.28

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: rs7153720; hg19: chr14-51280672;