chr3-133449982-A-AAGG

Variant names:

• chr3-133449982-A-AAGG
• rs1212404887
• NM_003571.4:c.730-320_730-319insGGA

Variant summary

Our verdict is Likely benign. The variant received -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
• Publications: 0 publications found

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

Our verdict: Likely_benign. The variant received -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 VariationId is 1241485.Status of the report is criteria_provided_single_submitter, 1 stars.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BFSP2	NM_003571.4	MANE Select	c.730-320_730-319insGGA		intron	N/A	NP_003562.1	Q13515
	BFSP2-AS1	NR_135276.2		n.344-1088_344-1087insCCT		intron	N/A
	BFSP2-AS1	NR_135277.2		n.344-4408_344-4407insCCT		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BFSP2	ENST00000302334.3	TSL:1 MANE Select	c.730-321_730-320insAGG		intron	N/A	ENSP00000304987.2	Q13515
	BFSP2-AS1	ENST00000515542.1	TSL:1	n.168-1088_168-1087insCCT		intron	N/A
	BFSP2	ENST00000511434.1	TSL:3	n.196-321_196-320insAGG		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0616 AC: 5273 AN: 85576 Hom.: 182 Cov.: 0

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

African (AFR) AF: 0.0660 AC: 1356 AN: 20530

American (AMR) AF: 0.0433 AC: 360 AN: 8322

Ashkenazi Jewish (ASJ) AF: 0.0757 AC: 156 AN: 2060

East Asian (EAS) AF: 0.0895 AC: 246 AN: 2748

South Asian (SAS) AF: 0.0307 AC: 61 AN: 1988

European-Finnish (FIN) AF: 0.0526 AC: 263 AN: 5002

Middle Eastern (MID) AF: 0.0714 AC: 11 AN: 154

European-Non Finnish (NFE) AF: 0.0628 AC: 2712 AN: 43162

Other (OTH) AF: 0.0770 AC: 85 AN: 1104

Alfa AF: 0.0511 Hom.: 30

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.0070
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs1212404887; hg19: chr3-133168826;