14-50725853-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Moderate BP6_Moderate BA1

The ENST00000382041.7(NIN):c.*19C>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00924 in 1,594,070 control chromosomes in the GnomAD database, including 1,083 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.047 (548 hom., cov: 31)
  • Exomes 𝑓: 0.0053 (535 hom.)
• Consequence: NIN ENST00000382041.7 3_prime_UTR
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.684

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=-0.34).
• BP6: Variant 14-50725853-G-C is Benign according to our data. Variant chr14-50725853-G-C is described in ClinVar as [Benign]. Clinvar id is 1261594.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIN	NM_020921.4	c.6192+100C>G		intron_variant		ENST00000530997.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIN	ENST00000530997.7	c.6192+100C>G		intron_variant		5	NM_020921.4	P2

Frequencies

GnomAD3 genomes AF: 0.0469 AC: 7124 AN: 152048 Hom.: 542 Cov.: 31

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0178

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000622

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.000779

Gnomad OTH AF: 0.0330

GnomAD3 exomes AF: 0.0126 AC: 3092 AN: 245360 Hom.: 207 AF XY: 0.00868 AC XY: 1152 AN XY: 132762

Gnomad AFR exome AF: 0.165

Gnomad AMR exome AF: 0.00885

Gnomad ASJ exome AF: 0.000313

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.000570

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000682

Gnomad OTH exome AF: 0.00708

GnomAD4 exome AF: 0.00525 AC: 7575 AN: 1441904 Hom.: 535 Cov.: 29 AF XY: 0.00465 AC XY: 3324 AN XY: 715004

Gnomad4 AFR exome AF: 0.174

Gnomad4 AMR exome AF: 0.00972

Gnomad4 ASJ exome AF: 0.000157

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.000780

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000580

Gnomad4 OTH exome AF: 0.0110

GnomAD4 genome AF: 0.0470 AC: 7158 AN: 152166 Hom.: 548 Cov.: 31 AF XY: 0.0453 AC XY: 3367 AN XY: 74394

Gnomad4 AFR AF: 0.163

Gnomad4 AMR AF: 0.0177

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000622

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000779

Gnomad4 OTH AF: 0.0327

Alfa AF: 0.0253 Hom.: 51

Bravo AF: 0.0534

Asia WGS AF: 0.0130 AC: 47 AN: 3474

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

May 14, 2021

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
Cadd	Benign	11
Dann	Benign	0.85

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: rs60995653; hg19: chr14-51192571;