rs10145182

Variant names:

• chr14-50809291-T-A
• rs10145182
• NM_020921.4:c.184-2473A>T

Your query was ambiguous. Multiple possible variants found:

• chr14-50809291-T-A
• chr14-50809291-T-C
• chr14-50809291-T-G

Variant summary

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

The NM_020921.4(NIN):​c.184-2473A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,986 control chromosomes in the GnomAD database, including 8,025 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 0.31 (8025 hom., cov: 31)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.46

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

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.393 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIN	NM_020921.4	c.184-2473A>T		intron_variant	Intron 3 of 30	ENST00000530997.7	NP_065972.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIN	ENST00000530997.7	c.184-2473A>T		intron_variant	Intron 3 of 30	5	NM_020921.4	ENSP00000436092.2

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46602 AN: 151866 Hom.: 8016 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.420

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.366

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.319

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

GnomAD4 genome AF: 0.307 AC: 46625 AN: 151986 Hom.: 8025 Cov.: 31 AF XY: 0.302 AC XY: 22427 AN XY: 74278

Gnomad4 AFR AF: 0.186 AC: 0.18643 AN: 0.18643

Gnomad4 AMR AF: 0.237 AC: 0.236794 AN: 0.236794

Gnomad4 ASJ AF: 0.420 AC: 0.419746 AN: 0.419746

Gnomad4 EAS AF: 0.132 AC: 0.131915 AN: 0.131915

Gnomad4 SAS AF: 0.368 AC: 0.36783 AN: 0.36783

Gnomad4 FIN AF: 0.313 AC: 0.312713 AN: 0.312713

Gnomad4 NFE AF: 0.397 AC: 0.397027 AN: 0.397027

Gnomad4 OTH AF: 0.322 AC: 0.322138 AN: 0.322138

Alfa AF: 0.210 Hom.: 484

Bravo AF: 0.293

Asia WGS AF: 0.237 AC: 829 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0010
DANN	Benign	0.49
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

Publications

LitVar

Other links and lift over

dbSNP: rs10145182; hg19: chr14-51276009;