rs6080717

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.1926C>T(p.Thr642Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.272 in 1,613,746 control chromosomes in the GnomAD database, including 61,767 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.26 ( 5329 hom., cov: 33)

Exomes 𝑓: 0.27 ( 56438 hom. )

Consequence

BFSP1
NM_001195.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: -2.33

Publications

15 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=-0.79).

BP6

Variant 20-17494146-G-A is Benign according to our data. Variant chr20-17494146-G-A is described in ClinVar as [Benign]. Clinvar id is 257616.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.33 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.284 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BFSP1	NM_001195.5 link	c.1926C>T	p.Thr642Thr	synonymous_variant	Exon 8 of 8	ENST00000377873.8	NP_001186.1	Q12934-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
BFSP1	ENST00000377873.8 link	c.1926C>T	p.Thr642Thr	synonymous_variant	Exon 8 of 8	1	NM_001195.5	ENSP00000367104.3	Q12934-1
BFSP1	ENST00000377868.6 link	c.1551C>T	p.Thr517Thr	synonymous_variant	Exon 8 of 8	1		ENSP00000367099.2	Q12934-2
BFSP1	ENST00000536626.7 link	c.1509C>T	p.Thr503Thr	synonymous_variant	Exon 9 of 9	2		ENSP00000442522.1	Q12934-3

Frequencies

GnomAD3 genomes

AF:

0.260

AC:

39460

AN:

151940

Hom.:

5323

Cov.:

show subpopulations

Gnomad AFR

AF:

0.253

Gnomad AMI

AF:

0.333

Gnomad AMR

AF:

0.241

Gnomad ASJ

AF:

0.264

Gnomad EAS

AF:

0.0644

Gnomad SAS

AF:

0.211

Gnomad FIN

AF:

0.250

Gnomad MID

AF:

0.272

Gnomad NFE

AF:

0.287

Gnomad OTH

AF:

0.255

GnomAD2 exomes

AF:

0.245

AC:

61620

AN:

251378

AF XY:

0.245

show subpopulations

Gnomad AFR exome

AF:

0.245

Gnomad AMR exome

AF:

0.243

Gnomad ASJ exome

AF:

0.274

Gnomad EAS exome

AF:

0.0583

Gnomad FIN exome

AF:

0.243

Gnomad NFE exome

AF:

0.284

Gnomad OTH exome

AF:

0.249

GnomAD4 exome

AF:

0.273

AC:

399063

AN:

1461688

Hom.:

56438

Cov.:

AF XY:

0.270

AC XY:

196693

AN XY:

727158

show subpopulations

African (AFR)

AF:

0.254

AC:

8510

AN:

33474

American (AMR)

AF:

0.239

AC:

10702

AN:

44722

Ashkenazi Jewish (ASJ)

AF:

0.273

AC:

7122

AN:

26134

East Asian (EAS)

AF:

0.0438

AC:

1738

AN:

39700

South Asian (SAS)

AF:

0.205

AC:

17680

AN:

86250

European-Finnish (FIN)

AF:

0.245

AC:

13060

AN:

53352

Middle Eastern (MID)

AF:

0.215

AC:

1238

AN:

5768

European-Non Finnish (NFE)

AF:

0.291

AC:

323612

AN:

1111896

Other (OTH)

AF:

0.255

AC:

15401

AN:

60392

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.470

Heterozygous variant carriers

16490

32979

49469

65958

82448

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.260

AC:

39485

AN:

152058

Hom.:

5329

Cov.:

AF XY:

0.257

AC XY:

19122

AN XY:

74326

show subpopulations

African (AFR)

AF:

0.253

AC:

10479

AN:

41466

American (AMR)

AF:

0.241

AC:

3685

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.264

AC:

917

AN:

3470

East Asian (EAS)

AF:

0.0639

AC:

331

AN:

5176

South Asian (SAS)

AF:

0.210

AC:

1013

AN:

4816

European-Finnish (FIN)

AF:

0.250

AC:

2635

AN:

10550

Middle Eastern (MID)

AF:

0.279

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.287

AC:

19503

AN:

67974

Other (OTH)

AF:

0.254

AC:

536

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1502

3004

4506

6008

7510

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.275

Hom.:

24118

Bravo

AF:

0.261

Asia WGS

AF:

0.172

AC:

602

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Apr 12, 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

- -

not specified

Benign:1

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Cataract 33

Benign:1

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

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

-0.79

CADD

Benign

0.11

(source)

DANN

Benign

0.72

PhyloP100

-2.3

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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rs6080717

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