dbSNP rs6650505: NIN:c.184-238T>C (chr14-50807056-A-G) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

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

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.603

Publications

3 publications found

Variant links:

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)

NIN links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_020921.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NIN	NM_020921.4	MANE Select	c.184-238T>C	intron	N/A	NP_065972.4
NIN	NM_182946.2		c.184-238T>C	intron	N/A	NP_891991.2	Q8N4C6-1
NIN	NM_182944.3		c.184-238T>C	intron	N/A	NP_891989.3	C9J066

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NIN	ENST00000530997.7	TSL:5 MANE Select	c.184-238T>C	intron	N/A	ENSP00000436092.2	Q8N4C6-7
NIN	ENST00000382041.7	TSL:1	c.184-238T>C	intron	N/A	ENSP00000371472.3	Q8N4C6-1
NIN	ENST00000382043.8	TSL:1	c.184-238T>C	intron	N/A	ENSP00000371474.4	Q8N4C6-11

Frequencies

GnomAD3 genomes

AF:

0.411

AC:

62374

AN:

151928

Hom.:

14156

Cov.:

show subpopulations

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.:

AF XY:

0.406

AC XY:

30151

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.244

AC:

10122

AN:

41470

American (AMR)

AF:

0.321

AC:

4903

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.573

AC:

1985

AN:

3466

East Asian (EAS)

AF:

0.241

AC:

1249

AN:

5174

South Asian (SAS)

AF:

0.445

AC:

2148

AN:

4824

European-Finnish (FIN)

AF:

0.455

AC:

4806

AN:

10552

Middle Eastern (MID)

AF:

0.486

AC:

143

AN:

294

European-Non Finnish (NFE)

AF:

0.524

AC:

35581

AN:

67962

Other (OTH)

AF:

0.443

AC:

936

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1764

3528

5291

7055

8819

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

594

1188

1782

2376

2970

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.489

Hom.:

31447

Bravo

AF:

0.390

Asia WGS

AF:

0.347

AC:

1211

AN:

3478

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.4

(source)

DANN

Benign

0.49

PhyloP100

0.60

PromoterAI

-0.016

Neutral

(source)

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over