Variant 20-17494146-G-A 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.1926C>T(p.Thr642=) 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

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
BFSP1	NM_001195.5 linkuse as main transcript	c.1926C>T	p.Thr642=	synonymous_variant	8/8	ENST00000377873.8	NP_001186.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
BFSP1	ENST00000377873.8 linkuse as main transcript	c.1926C>T	p.Thr642=	synonymous_variant	8/8	1	NM_001195.5	ENSP00000367104	P1	Q12934-1
BFSP1	ENST00000377868.6 linkuse as main transcript	c.1551C>T	p.Thr517=	synonymous_variant	8/8	1		ENSP00000367099		Q12934-2
BFSP1	ENST00000536626.7 linkuse as main transcript	c.1509C>T	p.Thr503=	synonymous_variant	9/9	2		ENSP00000442522		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

GnomAD3 exomes

AF:

0.245

AC:

61620

AN:

251378

Hom.:

8043

AF XY:

0.245

AC XY:

33231

AN XY:

135878

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 SAS exome

AF:

0.205

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

Gnomad4 AFR exome

AF:

0.254

Gnomad4 AMR exome

AF:

0.239

Gnomad4 ASJ exome

AF:

0.273

Gnomad4 EAS exome

AF:

0.0438

Gnomad4 SAS exome

AF:

0.205

Gnomad4 FIN exome

AF:

0.245

Gnomad4 NFE exome

AF:

0.291

Gnomad4 OTH exome

AF:

0.255

GnomAD4 genome

AF:

0.260

AC:

39485

AN:

152058

Hom.:

5329

Cov.:

AF XY:

0.257

AC XY:

19122

AN XY:

74326

show subpopulations

Gnomad4 AFR

AF:

0.253

Gnomad4 AMR

AF:

0.241

Gnomad4 ASJ

AF:

0.264

Gnomad4 EAS

AF:

0.0639

Gnomad4 SAS

AF:

0.210

Gnomad4 FIN

AF:

0.250

Gnomad4 NFE

AF:

0.287

Gnomad4 OTH

AF:

0.254

Alfa

AF:

0.277

Hom.:

11354

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

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
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. -

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

- -

Cataract 33

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 27, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.79

CADD

Benign

0.11

DANN

Benign

0.72

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