rs186263310

Variant summary

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

The ENST00000508053.6(FBN2):​c.-566+444T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0263 in 105,492 control chromosomes in the GnomAD database, including 548 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 0.026 ( 548 hom., cov: 23)

Consequence

FBN2
ENST00000508053.6 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0610
Variant links:
Genes affected
FBN2 (HGNC:3604): (fibrillin 2) The protein encoded by this gene is a component of connective tissue microfibrils and may be involved in elastic fiber assembly. Mutations in this gene cause congenital contractural arachnodactyly. [provided by RefSeq, Jul 2008]
SLC27A6 (HGNC:11000): (solute carrier family 27 member 6) This gene encodes a member of the fatty acid transport protein family (FATP). FATPs are involved in the uptake of long-chain fatty acids and have unique expression patterns. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

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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=-0.99).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0976 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FBN2ENST00000508053.6 linkc.-566+444T>C intron_variant Intron 5 of 14 5 ENSP00000424571.2 A0A9H4AZX0
SLC27A6ENST00000508645.5 linkc.-270+1975A>G intron_variant Intron 1 of 6 5 ENSP00000421759.1 D6RAJ2

Frequencies

GnomAD3 genomes
AF:
0.0263
AC:
2771
AN:
105480
Hom.:
548
Cov.:
23
show subpopulations
Gnomad AFR
AF:
0.101
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00924
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000213
Gnomad SAS
AF:
0.00257
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000564
Gnomad OTH
AF:
0.0205
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0263
AC:
2775
AN:
105492
Hom.:
548
Cov.:
23
AF XY:
0.0255
AC XY:
1281
AN XY:
50320
show subpopulations
Gnomad4 AFR
AF:
0.101
Gnomad4 AMR
AF:
0.00921
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000214
Gnomad4 SAS
AF:
0.00259
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000564
Gnomad4 OTH
AF:
0.0204
Alfa
AF:
0.0145
Hom.:
3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.99
CADD
Benign
3.5
DANN
Benign
0.25

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: rs186263310; hg19: chr5-127875736; API