NM_020921.4:c.184-7136G>A

Variant names:

• chr14-50813954-C-T
• rs7153720
• NM_020921.4:c.184-7136G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_020921.4(NIN):​c.184-7136G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.375 in 151,992 control chromosomes in the GnomAD database, including 12,169 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 0.38 (12169 hom., cov: 33)
• Consequence: NIN NM_020921.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 3 publications found

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]

NIN Gene-Disease associations (from GenCC):

• Seckel syndrome 7

  Inheritance: AR, Unknown Classification: LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.493 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NIN	NM_020921.4	c.184-7136G>A		intron_variant	Intron 3 of 30	ENST00000530997.7	NP_065972.4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NIN	ENST00000530997.7	c.184-7136G>A		intron_variant	Intron 3 of 30	5	NM_020921.4	ENSP00000436092.2

Frequencies

GnomAD3 genomes AF: 0.375 AC: 57000 AN: 151872 Hom.: 12165 Cov.: 33

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.239

Gnomad SAS AF: 0.405

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.402

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.380

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

GnomAD4 genome AF: 0.375 AC: 57017 AN: 151992 Hom.: 12169 Cov.: 33 AF XY: 0.371 AC XY: 27554 AN XY: 74292

African (AFR) AF: 0.189 AC: 7830 AN: 41472

American (AMR) AF: 0.288 AC: 4393 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1726 AN: 3470

East Asian (EAS) AF: 0.238 AC: 1232 AN: 5168

South Asian (SAS) AF: 0.406 AC: 1957 AN: 4824

European-Finnish (FIN) AF: 0.442 AC: 4655 AN: 10526

Middle Eastern (MID) AF: 0.401 AC: 118 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33786 AN: 67950

Other (OTH) AF: 0.383 AC: 809 AN: 2110

Alfa AF: 0.454 Hom.: 48681

Bravo AF: 0.354

Asia WGS AF: 0.322 AC: 1124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.039
DANN	Benign	0.28
PhyloP100		-1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs7153720; hg19: chr14-51280672;