2-112177474-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_153214.3(FBLN7):​c.532+1635G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.136 in 152,198 control chromosomes in the GnomAD database, including 1,641 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 0.14 ( 1641 hom., cov: 32)
Exomes 𝑓: 0.083 ( 0 hom. )

Consequence

FBLN7
NM_153214.3 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.355
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.326 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
FBLN7NM_153214.3 linkuse as main transcriptc.532+1635G>T intron_variant ENST00000331203.7 NP_694946.2 Q53RD9-1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
FBLN7ENST00000331203.7 linkuse as main transcriptc.532+1635G>T intron_variant 1 NM_153214.3 ENSP00000331411.2 Q53RD9-1

Frequencies

GnomAD3 genomes
AF:
0.136
AC:
20683
AN:
152056
Hom.:
1642
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0961
Gnomad AMI
AF:
0.160
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.156
Gnomad EAS
AF:
0.340
Gnomad SAS
AF:
0.101
Gnomad FIN
AF:
0.0624
Gnomad MID
AF:
0.111
Gnomad NFE
AF:
0.146
Gnomad OTH
AF:
0.139
GnomAD4 exome
AF:
0.0833
AC:
2
AN:
24
Hom.:
0
Cov.:
0
AF XY:
0.00
AC XY:
0
AN XY:
18
show subpopulations
Gnomad4 AFR exome
AF:
0.500
Gnomad4 FIN exome
AF:
0.250
Gnomad4 NFE exome
AF:
0.00
GnomAD4 genome
AF:
0.136
AC:
20691
AN:
152174
Hom.:
1641
Cov.:
32
AF XY:
0.135
AC XY:
10040
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0962
Gnomad4 AMR
AF:
0.187
Gnomad4 ASJ
AF:
0.156
Gnomad4 EAS
AF:
0.339
Gnomad4 SAS
AF:
0.101
Gnomad4 FIN
AF:
0.0624
Gnomad4 NFE
AF:
0.146
Gnomad4 OTH
AF:
0.140
Alfa
AF:
0.0841
Hom.:
109
Bravo
AF:
0.144
Asia WGS
AF:
0.209
AC:
727
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
3.1
DANN
Benign
0.62

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: rs4849049; hg19: chr2-112935051; API