rs12893300

chr14-50798735-C-T

Variant summary

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

The NM_020921.4(NIN):c.266-5854G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,156 control chromosomes in the GnomAD database, including 967 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 0.10 (967 hom., cov: 32)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

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=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.142 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NIN	NM_020921.4	c.266-5854G>A		intron_variant		ENST00000530997.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NIN	ENST00000530997.7	c.266-5854G>A		intron_variant		5	NM_020921.4	P2

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15461 AN: 152038 Hom.: 969 Cov.: 32

Gnomad AFR AF: 0.0256

Gnomad AMI AF: 0.0857

Gnomad AMR AF: 0.147

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.123

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.151

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.102 AC: 15461 AN: 152156 Hom.: 967 Cov.: 32 AF XY: 0.104 AC XY: 7740 AN XY: 74362

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.147

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.123

Gnomad4 SAS AF: 0.132

Gnomad4 FIN AF: 0.151

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.111

Alfa AF: 0.121 Hom.: 1509

Bravo AF: 0.0974

Asia WGS AF: 0.120 AC: 417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	2.1
Dann	Benign	0.61

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: rs12893300; hg19: chr14-51265453; COSMIC: COSV55380802; COSMIC: COSV55380802;