Genetic Variant NM_052966.4:c.*2746T>C (chr1-184792231-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_052966.4(NIBAN1):c.*2746T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.529 in 152,050 control chromosomes in the GnomAD database, including 22,278 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 0.53 ( 22277 hom., cov: 32)

Exomes 𝑓: 0.44 ( 1 hom. )

Consequence

NIBAN1
NM_052966.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.682

Publications

16 publications found

Variant links:

Genes affected

NIBAN1 (HGNC:16784): (niban apoptosis regulator 1) This gene encodes a member of the family with sequence similarity 129 protein family. This gene is highly expressed in several cancer cells and may serve as a prognostic marker for certain cancers. The encoded protein may play a role in regulating p53-mediated apoptosis. [provided by RefSeq, Sep 2016]

NIBAN1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.692 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_052966.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NIBAN1	NM_052966.4	MANE Select	c.*2746T>C		3_prime_UTR	Exon 14 of 14	NP_443198.1	Q9BZQ8

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
NIBAN1	ENST00000367511.4	TSL:1 MANE Select	c.*2746T>C	3_prime_UTR	Exon 14 of 14	ENSP00000356481.3	Q9BZQ8
NIBAN1	ENST00000899939.1		c.*2746T>C	3_prime_UTR	Exon 13 of 13	ENSP00000569998.1
NIBAN1	ENST00000899938.1		c.*2746T>C	3_prime_UTR	Exon 13 of 13	ENSP00000569997.1

Frequencies

GnomAD3 genomes

AF:

0.529

AC:

80291

AN:

151914

Hom.:

22252

Cov.:

show subpopulations

Gnomad AFR

AF:

0.698

Gnomad AMI

AF:

0.464

Gnomad AMR

AF:

0.460

Gnomad ASJ

AF:

0.422

Gnomad EAS

AF:

0.616

Gnomad SAS

AF:

0.529

Gnomad FIN

AF:

0.527

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.441

Gnomad OTH

AF:

0.505

GnomAD4 exome

AF:

0.444

AC:

AN:

Hom.:

Cov.:

AF XY:

0.417

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

0.750

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.357

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.483

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.529

AC:

80361

AN:

152032

Hom.:

22277

Cov.:

AF XY:

0.531

AC XY:

39503

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.698

AC:

28945

AN:

41452

American (AMR)

AF:

0.460

AC:

7026

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.422

AC:

1466

AN:

3470

East Asian (EAS)

AF:

0.616

AC:

3186

AN:

5170

South Asian (SAS)

AF:

0.530

AC:

2554

AN:

4820

European-Finnish (FIN)

AF:

0.527

AC:

5574

AN:

10568

Middle Eastern (MID)

AF:

0.500

AC:

147

AN:

294

European-Non Finnish (NFE)

AF:

0.441

AC:

29987

AN:

67964

Other (OTH)

AF:

0.500

AC:

1054

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1826

3651

5477

7302

9128

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

686

1372

2058

2744

3430

<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:

0.469

Hom.:

43726

Bravo

AF:

0.533

Asia WGS

AF:

0.573

AC:

1994

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.62

(source)

DANN

Benign

0.60

PhyloP100

-0.68

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