15-90877743-T-C

Variant names:

• chr15-90877743-T-C
• rs1573643
• NM_002569.4:c.667+128T>C

Variant summary

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

The NM_002569.4(FURIN):​c.667+128T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 694,376 control chromosomes in the GnomAD database, including 36,577 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 0.33 (8595 hom., cov: 33)
  • Exomes 𝑓: 0.31 (27982 hom.)
• Consequence: FURIN NM_002569.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 17 publications found

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]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.389 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002569.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FURIN	NM_002569.4	MANE Select	c.667+128T>C		intron	N/A	NP_002560.1
	FURIN	NM_001289823.2		c.667+128T>C		intron	N/A	NP_001276752.1
	FURIN	NM_001289824.2		c.667+128T>C		intron	N/A	NP_001276753.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FURIN	ENST00000268171.8	TSL:1 MANE Select	c.667+128T>C		intron	N/A	ENSP00000268171.2
	FURIN	ENST00000610579.4	TSL:5	c.667+128T>C		intron	N/A	ENSP00000484952.1
	FURIN	ENST00000618099.4	TSL:5	c.667+128T>C		intron	N/A	ENSP00000483552.1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49967 AN: 152026 Hom.: 8583 Cov.: 33

Gnomad AFR AF: 0.394

Gnomad AMI AF: 0.289

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.354

Gnomad EAS AF: 0.0936

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.259

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.331

GnomAD4 exome AF: 0.312 AC: 169238 AN: 542232 Hom.: 27982 AF XY: 0.312 AC XY: 87577 AN XY: 280730

African (AFR) AF: 0.398 AC: 5675 AN: 14250

American (AMR) AF: 0.199 AC: 4134 AN: 20774

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 5147 AN: 14634

East Asian (EAS) AF: 0.102 AC: 3125 AN: 30680

South Asian (SAS) AF: 0.280 AC: 13292 AN: 47444

European-Finnish (FIN) AF: 0.271 AC: 9001 AN: 33170

Middle Eastern (MID) AF: 0.347 AC: 1179 AN: 3398

European-Non Finnish (NFE) AF: 0.340 AC: 118593 AN: 348874

Other (OTH) AF: 0.313 AC: 9092 AN: 29008

GnomAD4 genome AF: 0.329 AC: 50007 AN: 152144 Hom.: 8595 Cov.: 33 AF XY: 0.322 AC XY: 23965 AN XY: 74390

African (AFR) AF: 0.394 AC: 16330 AN: 41486

American (AMR) AF: 0.263 AC: 4025 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.354 AC: 1228 AN: 3472

East Asian (EAS) AF: 0.0942 AC: 488 AN: 5180

South Asian (SAS) AF: 0.262 AC: 1263 AN: 4822

European-Finnish (FIN) AF: 0.259 AC: 2743 AN: 10602

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22873 AN: 67976

Other (OTH) AF: 0.330 AC: 698 AN: 2112

Alfa AF: 0.340 Hom.: 2118

Bravo AF: 0.330

Asia WGS AF: 0.209 AC: 728 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.5
DANN	Benign	0.50
PhyloP100		-0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1573643; hg19: chr15-91420973;