dbSNP rs1053993: BANF2:p.Thr78Ser (chr20-17735771-C-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_178477.5(BANF2):c.233C>G(p.Thr78Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.298 in 1,612,946 control chromosomes in the GnomAD database, including 74,199 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 9600 hom., cov: 32)

Exomes 𝑓: 0.29 ( 64599 hom. )

Consequence

BANF2
NM_178477.5 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.705

Publications

25 publications found

Variant links:

Genes affected

BANF2 (HGNC:16172): (BANF family member 2) Enables identical protein binding activity. Predicted to be involved in chromosome condensation and chromosome segregation. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

BANF2 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 (MetaRNN=7.073581E-4).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BANF2	NM_178477.5 link	c.233C>G	p.Thr78Ser	missense_variant	Exon 4 of 4	ENST00000246090.6	NP_848572.3	Q9H503-1A0A140VK85

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
BANF2	ENST00000246090.6 link	c.233C>G	p.Thr78Ser	missense_variant	Exon 4 of 4	1	NM_178477.5	ENSP00000246090.5	Q9H503-1
BANF2	ENST00000377805.7 link	c.233C>G	p.Thr78Ser	missense_variant	Exon 3 of 3	1		ENSP00000367036.3	Q9H503-1
BANF2	ENST00000545418.2 link	c.254C>G	p.Thr85Ser	missense_variant	Exon 3 of 3	3		ENSP00000439128.1	Q9H503-2
BANF2	ENST00000467330.1 link	n.437C>G		non_coding_transcript_exon_variant	Exon 2 of 2	3

Frequencies

GnomAD3 genomes

AF:

0.342

AC:

51870

AN:

151808

Hom.:

9596

Cov.:

show subpopulations

Gnomad AFR

AF:

0.483

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.267

Gnomad ASJ

AF:

0.236

Gnomad EAS

AF:

0.473

Gnomad SAS

AF:

0.352

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.244

Gnomad NFE

AF:

0.284

Gnomad OTH

AF:

0.315

GnomAD2 exomes

AF:

0.312

AC:

78419

AN:

251242

AF XY:

0.309

show subpopulations

Gnomad AFR exome

AF:

0.494

Gnomad AMR exome

AF:

0.277

Gnomad ASJ exome

AF:

0.224

Gnomad EAS exome

AF:

0.480

Gnomad FIN exome

AF:

0.268

Gnomad NFE exome

AF:

0.277

Gnomad OTH exome

AF:

0.284

GnomAD4 exome

AF:

0.294

AC:

428919

AN:

1461020

Hom.:

64599

Cov.:

AF XY:

0.294

AC XY:

213898

AN XY:

726814

show subpopulations

African (AFR)

AF:

0.493

AC:

16496

AN:

33448

American (AMR)

AF:

0.276

AC:

12336

AN:

44716

Ashkenazi Jewish (ASJ)

AF:

0.229

AC:

5994

AN:

26132

East Asian (EAS)

AF:

0.438

AC:

17388

AN:

39688

South Asian (SAS)

AF:

0.350

AC:

30163

AN:

86210

European-Finnish (FIN)

AF:

0.278

AC:

14840

AN:

53368

Middle Eastern (MID)

AF:

0.229

AC:

1312

AN:

5736

European-Non Finnish (NFE)

AF:

0.281

AC:

311967

AN:

1111358

Other (OTH)

AF:

0.305

AC:

18423

AN:

60364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.464

Heterozygous variant carriers

15787

31573

47360

63146

78933

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

10646

21292

31938

42584

53230

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.342

AC:

51903

AN:

151926

Hom.:

9600

Cov.:

AF XY:

0.339

AC XY:

25210

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.483

AC:

19972

AN:

41382

American (AMR)

AF:

0.267

AC:

4079

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.236

AC:

819

AN:

3470

East Asian (EAS)

AF:

0.474

AC:

2445

AN:

5158

South Asian (SAS)

AF:

0.352

AC:

1686

AN:

4794

European-Finnish (FIN)

AF:

0.264

AC:

2792

AN:

10578

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.284

AC:

19284

AN:

67962

Other (OTH)

AF:

0.312

AC:

656

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1697

3394

5090

6787

8484

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

512

1024

1536

2048

2560

<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:

0.289

Hom.:

4995

Bravo

AF:

0.348

TwinsUK

AF:

0.275

AC:

1019

ALSPAC

AF:

0.285

AC:

1098

ESP6500AA

AF:

0.491

AC:

2165

ESP6500EA

AF:

0.275

AC:

2368

ExAC

AF:

0.319

AC:

38761

Asia WGS

AF:

0.343

AC:

1191

AN:

3478

EpiCase

AF:

0.267

EpiControl

AF:

0.270

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.086

BayesDel_addAF

Benign

-0.68

BayesDel_noAF

Benign

-0.61

CADD

Benign

(source)

DANN

Benign

0.93

DEOGEN2

Benign

0.036

.;T;T

Eigen

Benign

-0.60

Eigen_PC

Benign

-0.52

FATHMM_MKL

Benign

0.0040

LIST_S2

Benign

0.15

T;.;T

MetaRNN

Benign

0.00071

T;T;T

MetaSVM

Benign

-0.92

PhyloP100

0.70

PrimateAI

Benign

0.38

PROVEAN

Benign

0.43

N;N;N

REVEL

Benign

0.050

Sift

Benign

0.34

T;T;T

Sift4G

Benign

0.74

T;T;T

Polyphen

0.0

.;B;B

Vest4

0.043

MutPred

0.30

.;Gain of disorder (P = 0.0465);Gain of disorder (P = 0.0465);

MPC

0.20

ClinPred

0.0024

GERP RS

3.4

Varity_R

0.058

gMVP

0.095

Mutation Taster

=99/1

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over