chr20-17494572-C-T

Variant names:

Variant summary

Our verdict is Benign. The variant received -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001195.5(BFSP1):c.1500G>A(p.Ala500Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.257 in 1,613,960 control chromosomes in the GnomAD database, including 55,506 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6243 hom., cov: 32)

Exomes 𝑓: 0.25 ( 49263 hom. )

Consequence

BFSP1
NM_001195.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:5

Conservation

PhyloP100: -0.104

Publications

21 publications found

Variant links:

Genes affected

BFSP1 (HGNC:1040): (beaded filament structural protein 1) This gene encodes a lens-specific intermediate filament-like protein named filensin. The encoded protein is expressed in lens fiber cells after differentiation has begun. This protein functions as a component of the beaded filament which is a cytoskeletal structure found in lens fiber cells. Mutations in this gene are the cause of autosomal recessive cortical juvenile-onset cataract. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

BFSP1 Gene-Disease associations (from GenCC):

cataract 33
Inheritance: AR, AD, SD Classification: STRONG, MODERATE, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
early-onset nuclear cataract
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

BFSP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BP6

Variant 20-17494572-C-T is Benign according to our data. Variant chr20-17494572-C-T is described in ClinVar as Benign. ClinVar VariationId is 257614.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.104 with no splicing effect.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BFSP1	NM_001195.5 link	c.1500G>A	p.Ala500Ala	synonymous_variant	Exon 8 of 8	ENST00000377873.8	NP_001186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
BFSP1	ENST00000377873.8 link	c.1500G>A	p.Ala500Ala	synonymous_variant	Exon 8 of 8	1	NM_001195.5	ENSP00000367104.3
BFSP1	ENST00000377868.6 link	c.1125G>A	p.Ala375Ala	synonymous_variant	Exon 8 of 8	1		ENSP00000367099.2
BFSP1	ENST00000536626.7 link	c.1083G>A	p.Ala361Ala	synonymous_variant	Exon 9 of 9	2		ENSP00000442522.1

Frequencies

GnomAD3 genomes

AF:

0.282

AC:

42851

AN:

151984

Hom.:

6218

Cov.:

show subpopulations

Gnomad AFR

AF:

0.336

Gnomad AMI

AF:

0.146

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.281

Gnomad EAS

AF:

0.394

Gnomad SAS

AF:

0.358

Gnomad FIN

AF:

0.218

Gnomad MID

AF:

0.261

Gnomad NFE

AF:

0.243

Gnomad OTH

AF:

0.289

GnomAD2 exomes

AF:

0.289

AC:

72649

AN:

251314

AF XY:

0.287

show subpopulations

Gnomad AFR exome

AF:

0.335

Gnomad AMR exome

AF:

0.349

Gnomad ASJ exome

AF:

0.290

Gnomad EAS exome

AF:

0.405

Gnomad FIN exome

AF:

0.221

Gnomad NFE exome

AF:

0.242

Gnomad OTH exome

AF:

0.268

GnomAD4 exome

AF:

0.255

AC:

372396

AN:

1461856

Hom.:

49263

Cov.:

AF XY:

0.258

AC XY:

187327

AN XY:

727232

show subpopulations

African (AFR)

AF:

0.344

AC:

11503

AN:

33480

American (AMR)

AF:

0.340

AC:

15226

AN:

44720

Ashkenazi Jewish (ASJ)

AF:

0.287

AC:

7513

AN:

26134

East Asian (EAS)

AF:

0.394

AC:

15622

AN:

39700

South Asian (SAS)

AF:

0.354

AC:

30516

AN:

86252

European-Finnish (FIN)

AF:

0.222

AC:

11855

AN:

53414

Middle Eastern (MID)

AF:

0.274

AC:

1580

AN:

5768

European-Non Finnish (NFE)

AF:

0.236

AC:

262272

AN:

1111992

Other (OTH)

AF:

0.270

AC:

16309

AN:

60396

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.474

Heterozygous variant carriers

19353

38705

58058

77410

96763

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

9122

18244

27366

36488

45610

<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:

0.282

AC:

42922

AN:

152104

Hom.:

6243

Cov.:

AF XY:

0.284

AC XY:

21142

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.337

AC:

13970

AN:

41496

American (AMR)

AF:

0.297

AC:

4544

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.281

AC:

972

AN:

3464

East Asian (EAS)

AF:

0.394

AC:

2037

AN:

5166

South Asian (SAS)

AF:

0.359

AC:

1732

AN:

4820

European-Finnish (FIN)

AF:

0.218

AC:

2310

AN:

10588

Middle Eastern (MID)

AF:

0.260

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.243

AC:

16539

AN:

67980

Other (OTH)

AF:

0.288

AC:

609

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1586

3173

4759

6346

7932

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

430

860

1290

1720

2150

<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:

0.258

Hom.:

10422

Bravo

AF:

0.287

Asia WGS

AF:

0.346

AC:

1206

AN:

3478

EpiCase

AF:

0.241

EpiControl

AF:

0.241

ClinVar

Significance: Benign

Submissions summary: Benign:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 02, 2018

GeneDx

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

Cataract 33

Benign:2

Jul 14, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Feb 02, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

3.7

(source)

DANN

Benign

0.40

PhyloP100

-0.10

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.030

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

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over