3-133448273-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_003571.4(BFSP2):​c.573-216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.101 in 152,196 control chromosomes in the GnomAD database, including 798 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 798 hom., cov: 32)

Consequence

BFSP2
NM_003571.4 intron

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.852
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-AS1 (HGNC:28425): (BFSP2 antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant 3-133448273-G-A is Benign according to our data. Variant chr3-133448273-G-A is described in ClinVar as [Benign]. Clinvar id is 1229325.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
BFSP2NM_003571.4 linkuse as main transcriptc.573-216G>A intron_variant ENST00000302334.3 NP_003562.1
BFSP2-AS1NR_135277.1 linkuse as main transcriptn.381-2698C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
BFSP2ENST00000302334.3 linkuse as main transcriptc.573-216G>A intron_variant 1 NM_003571.4 ENSP00000304987 P1
BFSP2-AS1ENST00000515542.1 linkuse as main transcriptn.282+508C>T intron_variant, non_coding_transcript_variant 1

Frequencies

GnomAD3 genomes
AF:
0.101
AC:
15339
AN:
152078
Hom.:
798
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0770
Gnomad AMI
AF:
0.0866
Gnomad AMR
AF:
0.0886
Gnomad ASJ
AF:
0.162
Gnomad EAS
AF:
0.180
Gnomad SAS
AF:
0.115
Gnomad FIN
AF:
0.0999
Gnomad MID
AF:
0.177
Gnomad NFE
AF:
0.107
Gnomad OTH
AF:
0.116
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.101
AC:
15336
AN:
152196
Hom.:
798
Cov.:
32
AF XY:
0.102
AC XY:
7606
AN XY:
74400
show subpopulations
Gnomad4 AFR
AF:
0.0769
Gnomad4 AMR
AF:
0.0884
Gnomad4 ASJ
AF:
0.162
Gnomad4 EAS
AF:
0.180
Gnomad4 SAS
AF:
0.114
Gnomad4 FIN
AF:
0.0999
Gnomad4 NFE
AF:
0.108
Gnomad4 OTH
AF:
0.115
Alfa
AF:
0.107
Hom.:
174
Bravo
AF:
0.100
Asia WGS
AF:
0.124
AC:
431
AN:
3478

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Benign, criteria provided, single submitterclinical testingGeneDxSep 05, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.86
CADD
Benign
0.52
DANN
Benign
0.61

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.

Other links and lift over

dbSNP: rs75186898; hg19: chr3-133167117; API