14-50803549-G-C

Position:

• chr14-50803549-G-C

Variant summary

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

The NM_020921.4(NIN):​c.265+3188C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 151,926 control chromosomes in the GnomAD database, including 20,853 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 0.51 (20853 hom., cov: 31)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.212

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.606 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NIN	NM_020921.4	c.265+3188C>G		intron_variant		ENST00000530997.7	NP_065972.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NIN	ENST00000530997.7	c.265+3188C>G		intron_variant		5	NM_020921.4	ENSP00000436092.2

Frequencies

GnomAD3 genomes AF: 0.513 AC: 77880 AN: 151808 Hom.: 20848 Cov.: 31

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.634

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.556

Gnomad SAS AF: 0.625

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.627

Gnomad NFE AF: 0.596

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.513 AC: 77912 AN: 151926 Hom.: 20853 Cov.: 31 AF XY: 0.511 AC XY: 37913 AN XY: 74244

Gnomad4 AFR AF: 0.375

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.557

Gnomad4 SAS AF: 0.624

Gnomad4 FIN AF: 0.534

Gnomad4 NFE AF: 0.596

Gnomad4 OTH AF: 0.546

Alfa AF: 0.406 Hom.: 1165

Bravo AF: 0.495

Asia WGS AF: 0.581 AC: 2023 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.59

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: rs9788504; hg19: chr14-51270267;