rs4849056

Variant names:

• chr2-112208932-G-A
• rs4849056
• XR_007069507.1:n.1219-12664G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_007069507.1(FBLN7):​n.1219-12664G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 152,044 control chromosomes in the GnomAD database, including 5,984 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.25 (5984 hom., cov: 31)
• Consequence: FBLN7 XR_007069507.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365
• Publications: 9 publications found

Genes affected

FBLN7 (HGNC:26740): (fibulin 7) Predicted to enable calcium ion binding activity; heparan sulfate proteoglycan binding activity; and heparin binding activity. Predicted to be involved in cell adhesion. Predicted to act upstream of or within positive regulation of biomineralization. Located in focal adhesion. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.347 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.253 AC: 38453 AN: 151926 Hom.: 5984 Cov.: 31

Gnomad AFR AF: 0.0698

Gnomad AMI AF: 0.173

Gnomad AMR AF: 0.236

Gnomad ASJ AF: 0.387

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.414

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.299

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

GnomAD4 genome AF: 0.253 AC: 38447 AN: 152044 Hom.: 5984 Cov.: 31 AF XY: 0.250 AC XY: 18581 AN XY: 74306

African (AFR) AF: 0.0697 AC: 2891 AN: 41502

American (AMR) AF: 0.236 AC: 3597 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.387 AC: 1342 AN: 3470

East Asian (EAS) AF: 0.242 AC: 1252 AN: 5164

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4810

European-Finnish (FIN) AF: 0.322 AC: 3394 AN: 10556

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23833 AN: 67954

Other (OTH) AF: 0.300 AC: 633 AN: 2112

Alfa AF: 0.321 Hom.: 26935

Bravo AF: 0.238

Asia WGS AF: 0.274 AC: 953 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	9.5
DANN	Benign	0.76
PhyloP100		0.36

Splicing

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

Other links and lift over

dbSNP: rs4849056; hg19: chr2-112966509;