3-133449982-A-AAGG

Position:

• chr3-133449982-A-AAGG

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_003571.4(BFSP2):​c.730-320_730-319insGGA variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.062 (183 hom., cov: 0)
  • Failed GnomAD Quality Control
• Consequence: BFSP2 NM_003571.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.00700

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)

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 3-133449982-A-AAGG is Benign according to our data. Variant chr3-133449982-A-AAGG is described in ClinVar as [Benign]. Clinvar id is 1241485.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BFSP2	NM_003571.4	c.730-320_730-319insGGA		intron_variant		ENST00000302334.3
BFSP2-AS1	NR_135277.1	n.381-4408_381-4407insCCT		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BFSP2	ENST00000302334.3	c.730-320_730-319insGGA		intron_variant		1	NM_003571.4	P1
BFSP2-AS1	ENST00000515542.1	n.168-1088_168-1087insCCT		intron_variant, non_coding_transcript_variant		1
BFSP2	ENST00000511434.1	n.196-320_196-319insGGA		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 5273 AN: 85576 Hom.: 182 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.0660

Gnomad AMI AF: 0.0441

Gnomad AMR AF: 0.0434

Gnomad ASJ AF: 0.0757

Gnomad EAS AF: 0.0892

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0526

Gnomad MID AF: 0.0765

Gnomad NFE AF: 0.0628

Gnomad OTH AF: 0.0786

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

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0616 AC: 5277 AN: 85682 Hom.: 183 Cov.: 0 AF XY: 0.0591 AC XY: 2355 AN XY: 39818

Gnomad4 AFR AF: 0.0660

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.0757

Gnomad4 EAS AF: 0.0895

Gnomad4 SAS AF: 0.0307

Gnomad4 FIN AF: 0.0526

Gnomad4 NFE AF: 0.0628

Gnomad4 OTH AF: 0.0770

Alfa AF: 0.0511 Hom.: 30

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jan 10, 2020

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1212404887; hg19: chr3-133168826;