Variant rs11537702 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_001195.5(BFSP1):c.804C>T(p.Asn268=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0709 in 1,614,044 control chromosomes in the GnomAD database, including 4,766 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.052 ( 286 hom., cov: 32)

Exomes 𝑓: 0.073 ( 4480 hom. )

Consequence

BFSP1
NM_001195.5 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:3

Conservation

PhyloP100: -2.64

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 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.77).

BP6

Variant 20-17498972-G-A is Benign according to our data. Variant chr20-17498972-G-A is described in ClinVar as [Benign]. Clinvar id is 257617.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-2.64 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0779 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BFSP1	NM_001195.5 linkuse as main transcript	c.804C>T	p.Asn268=	synonymous_variant	6/8	ENST00000377873.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BFSP1	ENST00000377873.8 linkuse as main transcript	c.804C>T	p.Asn268=	synonymous_variant	6/8	1	NM_001195.5	P1	Q12934-1
BFSP1	ENST00000377868.6 linkuse as main transcript	c.429C>T	p.Asn143=	synonymous_variant	6/8	1			Q12934-2
BFSP1	ENST00000536626.7 linkuse as main transcript	c.387C>T	p.Asn129=	synonymous_variant	7/9	2			Q12934-3

Frequencies

GnomAD3 genomes

AF:

0.0524

AC:

7975

AN:

152078

Hom.:

286

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0151

Gnomad AMI

AF:

0.0527

Gnomad AMR

AF:

0.0285

Gnomad ASJ

AF:

0.0418

Gnomad EAS

AF:

0.000193

Gnomad SAS

AF:

0.0228

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0475

Gnomad NFE

AF:

0.0796

Gnomad OTH

AF:

0.0463

GnomAD3 exomes

AF:

0.0551

AC:

13862

AN:

251466

Hom.:

576

AF XY:

0.0552

AC XY:

7507

AN XY:

135912

show subpopulations

Gnomad AFR exome

AF:

0.0129

Gnomad AMR exome

AF:

0.0235

Gnomad ASJ exome

AF:

0.0404

Gnomad EAS exome

AF:

0.000109

Gnomad SAS exome

AF:

0.0225

Gnomad FIN exome

AF:

0.102

Gnomad NFE exome

AF:

0.0808

Gnomad OTH exome

AF:

0.0565

GnomAD4 exome

AF:

0.0728

AC:

106476

AN:

1461848

Hom.:

4480

Cov.:

AF XY:

0.0715

AC XY:

51978

AN XY:

727224

show subpopulations

Gnomad4 AFR exome

AF:

0.0119

Gnomad4 AMR exome

AF:

0.0248

Gnomad4 ASJ exome

AF:

0.0400

Gnomad4 EAS exome

AF:

0.000126

Gnomad4 SAS exome

AF:

0.0239

Gnomad4 FIN exome

AF:

0.0992

Gnomad4 NFE exome

AF:

0.0833

Gnomad4 OTH exome

AF:

0.0626

GnomAD4 genome

AF:

0.0524

AC:

7974

AN:

152196

Hom.:

286

Cov.:

AF XY:

0.0524

AC XY:

3900

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.0150

Gnomad4 AMR

AF:

0.0284

Gnomad4 ASJ

AF:

0.0418

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0228

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0796

Gnomad4 OTH

AF:

0.0458

Alfa

AF:

0.0707

Hom.:

769

Bravo

AF:

0.0454

Asia WGS

AF:

0.0140

AC:

AN:

3478

EpiCase

AF:

0.0748

EpiControl

AF:

0.0695

ClinVar

Significance: Benign

Submissions summary: Benign:3

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Apr 12, 2018

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. -

Cataract 33

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.77

CADD

Benign

0.051

DANN

Benign

0.64

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over