rs6572697

chr14-50793083-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_020921.4(NIN):c.266-202C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.166 in 152,060 control chromosomes in the GnomAD database, including 2,365 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.17 (2365 hom., cov: 31)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.536

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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BP6: Variant 14-50793083-G-A is Benign according to our data. Variant chr14-50793083-G-A is described in ClinVar as [Benign]. Clinvar id is 1174330.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.195 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIN	NM_020921.4	c.266-202C>T		intron_variant		ENST00000530997.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIN	ENST00000530997.7	c.266-202C>T		intron_variant		5	NM_020921.4	P2

Frequencies

GnomAD3 genomes AF: 0.166 AC: 25190 AN: 151942 Hom.: 2366 Cov.: 31

Gnomad AFR AF: 0.0864

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.192

Gnomad ASJ AF: 0.241

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.197

Gnomad OTH AF: 0.184

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

GnomAD4 genome AF: 0.166 AC: 25203 AN: 152060 Hom.: 2365 Cov.: 31 AF XY: 0.166 AC XY: 12313 AN XY: 74316

Gnomad4 AFR AF: 0.0865

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.241

Gnomad4 EAS AF: 0.157

Gnomad4 SAS AF: 0.193

Gnomad4 FIN AF: 0.194

Gnomad4 NFE AF: 0.197

Gnomad4 OTH AF: 0.185

Alfa AF: 0.161 Hom.: 393

Bravo AF: 0.163

Asia WGS AF: 0.166 AC: 574 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Nov 12, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	2.2
Dann	Benign	0.62

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: rs6572697; hg19: chr14-51259801;