rs6650505

chr14-50807056-A-G

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.184-238T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.41 in 152,046 control chromosomes in the GnomAD database, including 14,159 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.41 (14159 hom., cov: 32)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.603

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=-0.84).
• BP6: Variant 14-50807056-A-G is Benign according to our data. Variant chr14-50807056-A-G is described in ClinVar as [Benign]. Clinvar id is 1252487.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIN	NM_020921.4	c.184-238T>C		intron_variant		ENST00000530997.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIN	ENST00000530997.7	c.184-238T>C		intron_variant		5	NM_020921.4	P2

Frequencies

GnomAD3 genomes AF: 0.411 AC: 62374 AN: 151928 Hom.: 14156 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.572

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.439

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

GnomAD4 genome AF: 0.410 AC: 62395 AN: 152046 Hom.: 14159 Cov.: 32 AF XY: 0.406 AC XY: 30151 AN XY: 74320

Gnomad4 AFR AF: 0.244

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.241

Gnomad4 SAS AF: 0.445

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.443

Alfa AF: 0.501 Hom.: 25637

Bravo AF: 0.390

Asia WGS AF: 0.347 AC: 1211 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

Jun 19, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.4
Dann	Benign	0.49

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: rs6650505; hg19: chr14-51273774;