Genetic Variant BFSP2:c.730-323G>A (chr3-133449980-G-A) – ACMG Classification: Benign (-14 pts)

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003571.4(BFSP2):c.730-323G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.15 ( 818 hom., cov: 16)

Consequence

BFSP2
NM_003571.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -2.09

Publications

0 publications found

Variant links:

Genes affected

BFSP2 (HGNC:1041): (beaded filament structural protein 2) More than 99% of the vertebrate ocular lens is comprised of terminally differentiated lens fiber cells. Two lens-specific intermediate filament-like proteins, the protein product of this gene (phakinin), and filensin, are expressed only after fiber cell differentiation has begun. Both proteins are found in a structurally unique cytoskeletal element that is referred to as the beaded filament (BF). Mutations in this gene have been associated with juvenile-onset, progressive cataracts and Dowling-Meara epidermolysis bullosa simplex. [provided by RefSeq, Jun 2009]

BFSP2 links:

BFSP2-AS1 (HGNC:28425): (BFSP2 antisense RNA 1)

BFSP2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-1.0).

BP6

Variant 3-133449980-G-A is Benign according to our data. Variant chr3-133449980-G-A is described in ClinVar as Benign. ClinVar VariationId is 1276319.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_003571.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BFSP2	NM_003571.4	MANE Select	c.730-323G>A	intron	N/A	NP_003562.1	Q13515
BFSP2-AS1	NR_135276.2		n.344-1085C>T	intron	N/A
BFSP2-AS1	NR_135277.2		n.344-4405C>T	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
BFSP2	ENST00000302334.3	TSL:1 MANE Select	c.730-323G>A	intron	N/A	ENSP00000304987.2	Q13515
BFSP2-AS1	ENST00000515542.1	TSL:1	n.168-1085C>T	intron	N/A
BFSP2	ENST00000511434.1	TSL:3	n.196-323G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.150

AC:

12690

AN:

84852

Hom.:

815

Cov.:

show subpopulations

Gnomad AFR

AF:

0.226

Gnomad AMI

AF:

0.0700

Gnomad AMR

AF:

0.119

Gnomad ASJ

AF:

0.0289

Gnomad EAS

AF:

0.0827

Gnomad SAS

AF:

0.0525

Gnomad FIN

AF:

0.195

Gnomad MID

AF:

0.0435

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.131

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.150

AC:

12712

AN:

84926

Hom.:

818

Cov.:

AF XY:

0.152

AC XY:

6053

AN XY:

39804

show subpopulations

African (AFR)

AF:

0.226

AC:

5700

AN:

25214

American (AMR)

AF:

0.119

AC:

861

AN:

7260

Ashkenazi Jewish (ASJ)

AF:

0.0289

AC:

AN:

2146

East Asian (EAS)

AF:

0.0825

AC:

232

AN:

2812

South Asian (SAS)

AF:

0.0516

AC:

AN:

1724

European-Finnish (FIN)

AF:

0.195

AC:

886

AN:

4544

Middle Eastern (MID)

AF:

0.0397

AC:

AN:

126

European-Non Finnish (NFE)

AF:

0.119

AC:

4708

AN:

39560

Other (OTH)

AF:

0.129

AC:

134

AN:

1040

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.419

Heterozygous variant carriers

380

760

1140

1520

1900

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

134

268

402

536

670

<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:

0.241

Hom.:

169

Asia WGS

AF:

0.0800

AC:

277

AN:

3464

ClinVar

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.39

(source)

DANN

Benign

0.29

PhyloP100

-2.1

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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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over