rs6227

Variant summary

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

The NM_002569.4(FURIN):​c.*124C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.288 in 709,594 control chromosomes in the GnomAD database, including 31,744 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 0.28 ( 6233 hom., cov: 33)
Exomes 𝑓: 0.29 ( 25511 hom. )

Consequence

FURIN
NM_002569.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.53
Variant links:
Genes affected
FURIN (HGNC:8568): (furin, paired basic amino acid cleaving enzyme) This gene encodes a member of the subtilisin-like proprotein convertase family, which includes proteases that process protein and peptide precursors trafficking through regulated or constitutive branches of the secretory pathway. It encodes a type 1 membrane bound protease that is expressed in many tissues, including neuroendocrine, liver, gut, and brain. The encoded protein undergoes an initial autocatalytic processing event in the ER and then sorts to the trans-Golgi network through endosomes where a second autocatalytic event takes place and the catalytic activity is acquired. Like other members of this convertase family, the product of this gene specifically cleaves substrates at single or paired basic residues. Some of its substrates include proparathyroid hormone, transforming growth factor beta 1 precursor, proalbumin, pro-beta-secretase, membrane type-1 matrix metalloproteinase, beta subunit of pro-nerve growth factor and von Willebrand factor. It is thought to be one of the proteases responsible for the activation of HIV envelope glycoproteins gp160 and gp140, and may play a role in tumor progression. Unlike SARS-CoV and other coronaviruses, the spike protein of SARS-CoV-2 is thought to be uniquely cleaved by this protease. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2020]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
FURINNM_002569.4 linkc.*124C>T 3_prime_UTR_variant Exon 16 of 16 ENST00000268171.8 NP_002560.1 P09958A0A024RC70

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
FURINENST00000268171.8 linkc.*124C>T 3_prime_UTR_variant Exon 16 of 16 1 NM_002569.4 ENSP00000268171.2 P09958

Frequencies

GnomAD3 genomes
AF:
0.280
AC:
42576
AN:
151976
Hom.:
6223
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.253
Gnomad AMI
AF:
0.286
Gnomad AMR
AF:
0.240
Gnomad ASJ
AF:
0.348
Gnomad EAS
AF:
0.0691
Gnomad SAS
AF:
0.222
Gnomad FIN
AF:
0.251
Gnomad MID
AF:
0.280
Gnomad NFE
AF:
0.327
Gnomad OTH
AF:
0.283
GnomAD4 exome
AF:
0.290
AC:
161870
AN:
557500
Hom.:
25511
Cov.:
7
AF XY:
0.289
AC XY:
83974
AN XY:
290128
show subpopulations
Gnomad4 AFR exome
AF:
0.253
Gnomad4 AMR exome
AF:
0.182
Gnomad4 ASJ exome
AF:
0.344
Gnomad4 EAS exome
AF:
0.0752
Gnomad4 SAS exome
AF:
0.237
Gnomad4 FIN exome
AF:
0.263
Gnomad4 NFE exome
AF:
0.326
Gnomad4 OTH exome
AF:
0.286
GnomAD4 genome
AF:
0.280
AC:
42609
AN:
152094
Hom.:
6233
Cov.:
33
AF XY:
0.274
AC XY:
20406
AN XY:
74346
show subpopulations
Gnomad4 AFR
AF:
0.254
Gnomad4 AMR
AF:
0.240
Gnomad4 ASJ
AF:
0.348
Gnomad4 EAS
AF:
0.0696
Gnomad4 SAS
AF:
0.221
Gnomad4 FIN
AF:
0.251
Gnomad4 NFE
AF:
0.327
Gnomad4 OTH
AF:
0.283
Alfa
AF:
0.318
Hom.:
4869
Bravo
AF:
0.277
Asia WGS
AF:
0.172
AC:
600
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.82
CADD
Benign
12
DANN
Benign
0.76

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: rs6227; hg19: chr15-91425232; COSMIC: COSV51579524; COSMIC: COSV51579524; API